help > FSL preprocessing + conn
Showing 1-9 of 9 posts
Nov 28, 2017 07:11 PM | Harrison Fisher - Martinos Center
FSL preprocessing + conn
Hello,
I have fMRI data preprocessed in FSL for GLM analysis using feat and I would also like to run connectivity analysis. Is there a way to generate and load in files that would normally be created by conn preprocessing to add the covariates that conn preprocessing automatically generates? (i.e. realignment, head motion etc.).
The bold images were preprocessed with the following:
RETROICOR
Slice Timing correction
Motion Correction
Topup correction
The bold images were then skull stripped with BET.
I also have already run free surfer on all the mprage images and used bbregister, flirt and fnirt to align the structural to functional images and the standard (MNI152 1mm) to the structural.
Any advice appreciated!
Thanks
- Harris
Napadow Lab
Martinos Center
I have fMRI data preprocessed in FSL for GLM analysis using feat and I would also like to run connectivity analysis. Is there a way to generate and load in files that would normally be created by conn preprocessing to add the covariates that conn preprocessing automatically generates? (i.e. realignment, head motion etc.).
The bold images were preprocessed with the following:
RETROICOR
Slice Timing correction
Motion Correction
Topup correction
The bold images were then skull stripped with BET.
I also have already run free surfer on all the mprage images and used bbregister, flirt and fnirt to align the structural to functional images and the standard (MNI152 1mm) to the structural.
Any advice appreciated!
Thanks
- Harris
Napadow Lab
Martinos Center
Nov 29, 2017 12:11 AM | Alfonso Nieto-Castanon - Boston University
RE: FSL preprocessing + conn
Hi Harris,
The preprocessing steps sound perfectly fine. You may simply:
a) import your fully-preprocessed MNI-space functional and structural data in the functional and structural tabs, respectively
b) if you have used mcflirt for motion correction enter the resulting .par files in CONN first-level covariates tab as a new covariate named 'realignment'
c) if you have used fsl_motion_outliers for outlier estimation enter the resulting regressor file also as a new first-level covariate now named 'scrubbing' (if you have not run any outlier estimation you may do so from CONN preprocessing tab -select 'functional outlier detection'- on your current data, which will automatically create the 'scrubbing' covariate for you)
After this, you may run any additional preprocessing steps directly from CONN (e.g. spatial smoothing), or you may skip that and proceed directly to the Denoising step. I would probably leave the default Denoising settings (alternatively you may choose to skip aCompCor -e.g. simply by removing the CSF and WhiteMatter ROIs from the 'confounds' list- if you find that somewhat redundant with the Retroicor step you have already run) and from that point on you may proceed normally.
Hope this helps
Alfonso
Originally posted by Harrison Fisher:
The preprocessing steps sound perfectly fine. You may simply:
a) import your fully-preprocessed MNI-space functional and structural data in the functional and structural tabs, respectively
b) if you have used mcflirt for motion correction enter the resulting .par files in CONN first-level covariates tab as a new covariate named 'realignment'
c) if you have used fsl_motion_outliers for outlier estimation enter the resulting regressor file also as a new first-level covariate now named 'scrubbing' (if you have not run any outlier estimation you may do so from CONN preprocessing tab -select 'functional outlier detection'- on your current data, which will automatically create the 'scrubbing' covariate for you)
After this, you may run any additional preprocessing steps directly from CONN (e.g. spatial smoothing), or you may skip that and proceed directly to the Denoising step. I would probably leave the default Denoising settings (alternatively you may choose to skip aCompCor -e.g. simply by removing the CSF and WhiteMatter ROIs from the 'confounds' list- if you find that somewhat redundant with the Retroicor step you have already run) and from that point on you may proceed normally.
Hope this helps
Alfonso
Originally posted by Harrison Fisher:
Hello,
I have fMRI data preprocessed in FSL for GLM analysis using feat and I would also like to run connectivity analysis. Is there a way to generate and load in files that would normally be created by conn preprocessing to add the covariates that conn preprocessing automatically generates? (i.e. realignment, head motion etc.).
The bold images were preprocessed with the following:
RETROICOR
Slice Timing correction
Motion Correction
Topup correction
The bold images were then skull stripped with BET.
I also have already run free surfer on all the mprage images and used bbregister, flirt and fnirt to align the structural to functional images and the standard (MNI152 1mm) to the structural.
Any advice appreciated!
Thanks
- Harris
Napadow Lab
Martinos Center
I have fMRI data preprocessed in FSL for GLM analysis using feat and I would also like to run connectivity analysis. Is there a way to generate and load in files that would normally be created by conn preprocessing to add the covariates that conn preprocessing automatically generates? (i.e. realignment, head motion etc.).
The bold images were preprocessed with the following:
RETROICOR
Slice Timing correction
Motion Correction
Topup correction
The bold images were then skull stripped with BET.
I also have already run free surfer on all the mprage images and used bbregister, flirt and fnirt to align the structural to functional images and the standard (MNI152 1mm) to the structural.
Any advice appreciated!
Thanks
- Harris
Napadow Lab
Martinos Center
Nov 30, 2017 08:11 PM | Harrison Fisher - Martinos Center
RE: FSL preprocessing + conn
Thank you very much Alfonso!
Just double checking: the RETROICOR files have to uploaded as first level covariates during setup, and then selected as confounds for denoising, correct? The script generates files with a *.1D extension, but conn doesn't seem to recognize those, but converting to *.txt seems to work for loading in the RETROICOR files.
On another note, is there a preferred/simplest method for exporting seed-voxel BETA values at the single subject level to a .txt or .mat format? I know there's a load_nifiti matlab function that could work, but wanted to see if you (or the conn toolbox) has a better implementation.
Best,
- Harris
Just double checking: the RETROICOR files have to uploaded as first level covariates during setup, and then selected as confounds for denoising, correct? The script generates files with a *.1D extension, but conn doesn't seem to recognize those, but converting to *.txt seems to work for loading in the RETROICOR files.
On another note, is there a preferred/simplest method for exporting seed-voxel BETA values at the single subject level to a .txt or .mat format? I know there's a load_nifiti matlab function that could work, but wanted to see if you (or the conn toolbox) has a better implementation.
Best,
- Harris
Jun 17, 2020 10:06 AM | Giuseppe Pontillo
RE: FSL preprocessing + conn
Dear CONN experts,
I'm trying to import preprocessed rs-fMRI data into CONN for subsequent analyses.
The data have been preprocessed according to FSL's melodic pipeline (which included motion correction with mcflirt, topup-based EPI distortion correction, high-pass filtering and no slice-timing correction since these are multiband, HCP-style fMRI data) followed by ICA-based denoising using FSL's ICA-AROMA.
I managed to import MNI-space structural data, as well as segmented tissue maps, motion parameters derived from mcflirt and outliers estimated by fsl_motion_outliers for the subsequent step.
Unfortunately, when trying to import precprocessed fMRI data as the primary functional dataset, I get the following error:
ERROR DESCRIPTION:
Error using conn_menu>conn_spm_read_vols (line 1091)
Error reading file C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii. File may have been modified or relocated. Please load file again
Error in conn_menu (line 656)
[temp,volhdr]=conn_spm_read_vols(title(n));
Error in conn (line 2049)
conn_menu('updateimage',CONN_h.menus.m_setup_00{5},cfile{3});
Error in conn_filesearchtool (line 222)
if length(h.callback)>1, feval(h.callback{1},h.callback{2:end},names); else, feval(h.callback{1},names); end
Am I missing something?
Once I manage to import the data, my idea is to go through functional smoothing and denoising before statistical analyses, do you suggest any additional step?
Thanks in advance for your precious help,
Giuseppe
I'm trying to import preprocessed rs-fMRI data into CONN for subsequent analyses.
The data have been preprocessed according to FSL's melodic pipeline (which included motion correction with mcflirt, topup-based EPI distortion correction, high-pass filtering and no slice-timing correction since these are multiband, HCP-style fMRI data) followed by ICA-based denoising using FSL's ICA-AROMA.
I managed to import MNI-space structural data, as well as segmented tissue maps, motion parameters derived from mcflirt and outliers estimated by fsl_motion_outliers for the subsequent step.
Unfortunately, when trying to import precprocessed fMRI data as the primary functional dataset, I get the following error:
ERROR DESCRIPTION:
Error using conn_menu>conn_spm_read_vols (line 1091)
Error reading file C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii. File may have been modified or relocated. Please load file again
Error in conn_menu (line 656)
[temp,volhdr]=conn_spm_read_vols(title(n));
Error in conn (line 2049)
conn_menu('updateimage',CONN_h.menus.m_setup_00{5},cfile{3});
Error in conn_filesearchtool (line 222)
if length(h.callback)>1, feval(h.callback{1},h.callback{2:end},names); else, feval(h.callback{1},names); end
Am I missing something?
Once I manage to import the data, my idea is to go through functional smoothing and denoising before statistical analyses, do you suggest any additional step?
Thanks in advance for your precious help,
Giuseppe
Jun 18, 2020 01:06 PM | Alfonso Nieto-Castanon - Boston University
RE: FSL preprocessing + conn
Dear Giuseppe,
That error seems to indicate some general/unspecified problem with the denoised_func_data_standard.nii file. Can you please check whether you are able to open/view that file in SPM or some other software? (e.g. use
spm_check_registration 'C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii'
Best
Alfonso
Originally posted by Giuseppe Pontillo:
That error seems to indicate some general/unspecified problem with the denoised_func_data_standard.nii file. Can you please check whether you are able to open/view that file in SPM or some other software? (e.g. use
spm_check_registration 'C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii'
Best
Alfonso
Originally posted by Giuseppe Pontillo:
Dear CONN experts,
I'm trying to import preprocessed rs-fMRI data into CONN for subsequent analyses.
The data have been preprocessed according to FSL's melodic pipeline (which included motion correction with mcflirt, topup-based EPI distortion correction, high-pass filtering and no slice-timing correction since these are multiband, HCP-style fMRI data) followed by ICA-based denoising using FSL's ICA-AROMA.
I managed to import MNI-space structural data, as well as segmented tissue maps, motion parameters derived from mcflirt and outliers estimated by fsl_motion_outliers for the subsequent step.
Unfortunately, when trying to import precprocessed fMRI data as the primary functional dataset, I get the following error:
ERROR DESCRIPTION:
Error using conn_menu>conn_spm_read_vols (line 1091)
Error reading file C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii. File may have been modified or relocated. Please load file again
Error in conn_menu (line 656)
[temp,volhdr]=conn_spm_read_vols(title(n));
Error in conn (line 2049)
conn_menu('updateimage',CONN_h.menus.m_setup_00{5},cfile{3});
Error in conn_filesearchtool (line 222)
if length(h.callback)>1, feval(h.callback{1},h.callback{2:end},names); else, feval(h.callback{1},names); end
Am I missing something?
Once I manage to import the data, my idea is to go through functional smoothing and denoising before statistical analyses, do you suggest any additional step?
Thanks in advance for your precious help,
Giuseppe
I'm trying to import preprocessed rs-fMRI data into CONN for subsequent analyses.
The data have been preprocessed according to FSL's melodic pipeline (which included motion correction with mcflirt, topup-based EPI distortion correction, high-pass filtering and no slice-timing correction since these are multiband, HCP-style fMRI data) followed by ICA-based denoising using FSL's ICA-AROMA.
I managed to import MNI-space structural data, as well as segmented tissue maps, motion parameters derived from mcflirt and outliers estimated by fsl_motion_outliers for the subsequent step.
Unfortunately, when trying to import precprocessed fMRI data as the primary functional dataset, I get the following error:
ERROR DESCRIPTION:
Error using conn_menu>conn_spm_read_vols (line 1091)
Error reading file C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii. File may have been modified or relocated. Please load file again
Error in conn_menu (line 656)
[temp,volhdr]=conn_spm_read_vols(title(n));
Error in conn (line 2049)
conn_menu('updateimage',CONN_h.menus.m_setup_00{5},cfile{3});
Error in conn_filesearchtool (line 222)
if length(h.callback)>1, feval(h.callback{1},h.callback{2:end},names); else, feval(h.callback{1},names); end
Am I missing something?
Once I manage to import the data, my idea is to go through functional smoothing and denoising before statistical analyses, do you suggest any additional step?
Thanks in advance for your precious help,
Giuseppe
Jun 20, 2020 06:06 PM | Giuseppe Pontillo
RE: FSL preprocessing + conn
Dear Alfonso,
thank you so much for your feedback.
Indeed, while I'm able to open/view that file in mricron or fsleyes, I cannot view it in SPM.
This is the error I get when trying to display the file in SPM:
Cannot access file "C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii".
Error using spm_slice_vol
Cant map view of file. It may be locked by another program.
Strangely enough, SPM is perfectly able to open the preprocessd fMRI dataset in the subject's native space ("denoised_func_data_noaggr.nii"), before applying spatial transformations with the following command:
applywarp -i denoised_func_data_nonaggr.nii -r standard.nii --premat=example_func2highres.mat -w highres2standard_warp.nii -v -o denoised_func_data_standard.nii
Am I missing something?
Originally posted by Alfonso Nieto-Castanon:
thank you so much for your feedback.
Indeed, while I'm able to open/view that file in mricron or fsleyes, I cannot view it in SPM.
This is the error I get when trying to display the file in SPM:
Cannot access file "C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii".
Error using spm_slice_vol
Cant map view of file. It may be locked by another program.
Strangely enough, SPM is perfectly able to open the preprocessd fMRI dataset in the subject's native space ("denoised_func_data_noaggr.nii"), before applying spatial transformations with the following command:
applywarp -i denoised_func_data_nonaggr.nii -r standard.nii --premat=example_func2highres.mat -w highres2standard_warp.nii -v -o denoised_func_data_standard.nii
Am I missing something?
Originally posted by Alfonso Nieto-Castanon:
Dear Giuseppe,
That error seems to indicate some general/unspecified problem with the denoised_func_data_standard.nii file. Can you please check whether you are able to open/view that file in SPM or some other software? (e.g. use
spm_check_registration 'C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii'
Best
Alfonso
Originally posted by Giuseppe Pontillo:
That error seems to indicate some general/unspecified problem with the denoised_func_data_standard.nii file. Can you please check whether you are able to open/view that file in SPM or some other software? (e.g. use
spm_check_registration 'C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii'
Best
Alfonso
Originally posted by Giuseppe Pontillo:
Dear CONN experts,
I'm trying to import preprocessed rs-fMRI data into CONN for subsequent analyses.
The data have been preprocessed according to FSL's melodic pipeline (which included motion correction with mcflirt, topup-based EPI distortion correction, high-pass filtering and no slice-timing correction since these are multiband, HCP-style fMRI data) followed by ICA-based denoising using FSL's ICA-AROMA.
I managed to import MNI-space structural data, as well as segmented tissue maps, motion parameters derived from mcflirt and outliers estimated by fsl_motion_outliers for the subsequent step.
Unfortunately, when trying to import precprocessed fMRI data as the primary functional dataset, I get the following error:
ERROR DESCRIPTION:
Error using conn_menu>conn_spm_read_vols (line 1091)
Error reading file C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii. File may have been modified or relocated. Please load file again
Error in conn_menu (line 656)
[temp,volhdr]=conn_spm_read_vols(title(n));
Error in conn (line 2049)
conn_menu('updateimage',CONN_h.menus.m_setup_00{5},cfile{3});
Error in conn_filesearchtool (line 222)
if length(h.callback)>1, feval(h.callback{1},h.callback{2:end},names); else, feval(h.callback{1},names); end
Am I missing something?
Once I manage to import the data, my idea is to go through functional smoothing and denoising before statistical analyses, do you suggest any additional step?
Thanks in advance for your precious help,
Giuseppe
I'm trying to import preprocessed rs-fMRI data into CONN for subsequent analyses.
The data have been preprocessed according to FSL's melodic pipeline (which included motion correction with mcflirt, topup-based EPI distortion correction, high-pass filtering and no slice-timing correction since these are multiband, HCP-style fMRI data) followed by ICA-based denoising using FSL's ICA-AROMA.
I managed to import MNI-space structural data, as well as segmented tissue maps, motion parameters derived from mcflirt and outliers estimated by fsl_motion_outliers for the subsequent step.
Unfortunately, when trying to import precprocessed fMRI data as the primary functional dataset, I get the following error:
ERROR DESCRIPTION:
Error using conn_menu>conn_spm_read_vols (line 1091)
Error reading file C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii. File may have been modified or relocated. Please load file again
Error in conn_menu (line 656)
[temp,volhdr]=conn_spm_read_vols(title(n));
Error in conn (line 2049)
conn_menu('updateimage',CONN_h.menus.m_setup_00{5},cfile{3});
Error in conn_filesearchtool (line 222)
if length(h.callback)>1, feval(h.callback{1},h.callback{2:end},names); else, feval(h.callback{1},names); end
Am I missing something?
Once I manage to import the data, my idea is to go through functional smoothing and denoising before statistical analyses, do you suggest any additional step?
Thanks in advance for your precious help,
Giuseppe
Jun 21, 2020 09:06 AM | Giuseppe Pontillo
RE: FSL preprocessing + conn
I think I figured it out: it was a
file size issue https://en.wikibooks.org/wiki/SPM/Workin...
The 4D fMRI dataset is really large (600 timepoints, about 2 GB).
Do you have any solutions (I'm working on a Windows 64-bit, 32GB RAM PC)?
Originally posted by Giuseppe Pontillo:
The 4D fMRI dataset is really large (600 timepoints, about 2 GB).
Do you have any solutions (I'm working on a Windows 64-bit, 32GB RAM PC)?
Originally posted by Giuseppe Pontillo:
Dear
Alfonso,
thank you so much for your feedback.
Indeed, while I'm able to open/view that file in mricron or fsleyes, I cannot view it in SPM.
This is the error I get when trying to display the file in SPM:
Cannot access file "C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii".
Error using spm_slice_vol
Cant map view of file. It may be locked by another program.
Strangely enough, SPM is perfectly able to open the preprocessd fMRI dataset in the subject's native space ("denoised_func_data_noaggr.nii"), before applying spatial transformations with the following command:
applywarp -i denoised_func_data_nonaggr.nii -r standard.nii --premat=example_func2highres.mat -w highres2standard_warp.nii -v -o denoised_func_data_standard.nii
Am I missing something?
Originally posted by Alfonso Nieto-Castanon:
thank you so much for your feedback.
Indeed, while I'm able to open/view that file in mricron or fsleyes, I cannot view it in SPM.
This is the error I get when trying to display the file in SPM:
Cannot access file "C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii".
Error using spm_slice_vol
Cant map view of file. It may be locked by another program.
Strangely enough, SPM is perfectly able to open the preprocessd fMRI dataset in the subject's native space ("denoised_func_data_noaggr.nii"), before applying spatial transformations with the following command:
applywarp -i denoised_func_data_nonaggr.nii -r standard.nii --premat=example_func2highres.mat -w highres2standard_warp.nii -v -o denoised_func_data_standard.nii
Am I missing something?
Originally posted by Alfonso Nieto-Castanon:
Dear Giuseppe,
That error seems to indicate some general/unspecified problem with the denoised_func_data_standard.nii file. Can you please check whether you are able to open/view that file in SPM or some other software? (e.g. use
spm_check_registration 'C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii'
Best
Alfonso
Originally posted by Giuseppe Pontillo:
That error seems to indicate some general/unspecified problem with the denoised_func_data_standard.nii file. Can you please check whether you are able to open/view that file in SPM or some other software? (e.g. use
spm_check_registration 'C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii'
Best
Alfonso
Originally posted by Giuseppe Pontillo:
Dear CONN experts,
I'm trying to import preprocessed rs-fMRI data into CONN for subsequent analyses.
The data have been preprocessed according to FSL's melodic pipeline (which included motion correction with mcflirt, topup-based EPI distortion correction, high-pass filtering and no slice-timing correction since these are multiband, HCP-style fMRI data) followed by ICA-based denoising using FSL's ICA-AROMA.
I managed to import MNI-space structural data, as well as segmented tissue maps, motion parameters derived from mcflirt and outliers estimated by fsl_motion_outliers for the subsequent step.
Unfortunately, when trying to import precprocessed fMRI data as the primary functional dataset, I get the following error:
ERROR DESCRIPTION:
Error using conn_menu>conn_spm_read_vols (line 1091)
Error reading file C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii. File may have been modified or relocated. Please load file again
Error in conn_menu (line 656)
[temp,volhdr]=conn_spm_read_vols(title(n));
Error in conn (line 2049)
conn_menu('updateimage',CONN_h.menus.m_setup_00{5},cfile{3});
Error in conn_filesearchtool (line 222)
if length(h.callback)>1, feval(h.callback{1},h.callback{2:end},names); else, feval(h.callback{1},names); end
Am I missing something?
Once I manage to import the data, my idea is to go through functional smoothing and denoising before statistical analyses, do you suggest any additional step?
Thanks in advance for your precious help,
Giuseppe
I'm trying to import preprocessed rs-fMRI data into CONN for subsequent analyses.
The data have been preprocessed according to FSL's melodic pipeline (which included motion correction with mcflirt, topup-based EPI distortion correction, high-pass filtering and no slice-timing correction since these are multiband, HCP-style fMRI data) followed by ICA-based denoising using FSL's ICA-AROMA.
I managed to import MNI-space structural data, as well as segmented tissue maps, motion parameters derived from mcflirt and outliers estimated by fsl_motion_outliers for the subsequent step.
Unfortunately, when trying to import precprocessed fMRI data as the primary functional dataset, I get the following error:
ERROR DESCRIPTION:
Error using conn_menu>conn_spm_read_vols (line 1091)
Error reading file C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii. File may have been modified or relocated. Please load file again
Error in conn_menu (line 656)
[temp,volhdr]=conn_spm_read_vols(title(n));
Error in conn (line 2049)
conn_menu('updateimage',CONN_h.menus.m_setup_00{5},cfile{3});
Error in conn_filesearchtool (line 222)
if length(h.callback)>1, feval(h.callback{1},h.callback{2:end},names); else, feval(h.callback{1},names); end
Am I missing something?
Once I manage to import the data, my idea is to go through functional smoothing and denoising before statistical analyses, do you suggest any additional step?
Thanks in advance for your precious help,
Giuseppe
Jun 22, 2020 12:06 AM | Alfonso Nieto-Castanon - Boston University
RE: FSL preprocessing + conn
Hi Giuseppe,
A couple of "easier" things to try first would be to: a) restart your computer (if the file has been locked by some other concurrent Windows process this should unlock it); and/or b) copy the file to a different folder (same reasoning as before). If none of this works and the issue is really related to the file size, another possibility would be to resample the file using int16 encoding (dt = [4 0]), which should result in a file of approximately 1Gb (assuming 600 timepoints and 2mm isotropic voxels)
Hope this helps
Alfonso
Originally posted by Giuseppe Pontillo:
A couple of "easier" things to try first would be to: a) restart your computer (if the file has been locked by some other concurrent Windows process this should unlock it); and/or b) copy the file to a different folder (same reasoning as before). If none of this works and the issue is really related to the file size, another possibility would be to resample the file using int16 encoding (dt = [4 0]), which should result in a file of approximately 1Gb (assuming 600 timepoints and 2mm isotropic voxels)
Hope this helps
Alfonso
Originally posted by Giuseppe Pontillo:
I think I figured
it out: it was a file size issue https://en.wikibooks.org/wiki/SPM/Workin...
The 4D fMRI dataset is really large (600 timepoints, about 2 GB).
Do you have any solutions (I'm working on a Windows 64-bit, 32GB RAM PC)?
Originally posted by Giuseppe Pontillo:
The 4D fMRI dataset is really large (600 timepoints, about 2 GB).
Do you have any solutions (I'm working on a Windows 64-bit, 32GB RAM PC)?
Originally posted by Giuseppe Pontillo:
Dear
Alfonso,
thank you so much for your feedback.
Indeed, while I'm able to open/view that file in mricron or fsleyes, I cannot view it in SPM.
This is the error I get when trying to display the file in SPM:
Cannot access file "C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii".
Error using spm_slice_vol
Cant map view of file. It may be locked by another program.
Strangely enough, SPM is perfectly able to open the preprocessd fMRI dataset in the subject's native space ("denoised_func_data_noaggr.nii"), before applying spatial transformations with the following command:
applywarp -i denoised_func_data_nonaggr.nii -r standard.nii --premat=example_func2highres.mat -w highres2standard_warp.nii -v -o denoised_func_data_standard.nii
Am I missing something?
Originally posted by Alfonso Nieto-Castanon:
thank you so much for your feedback.
Indeed, while I'm able to open/view that file in mricron or fsleyes, I cannot view it in SPM.
This is the error I get when trying to display the file in SPM:
Cannot access file "C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii".
Error using spm_slice_vol
Cant map view of file. It may be locked by another program.
Strangely enough, SPM is perfectly able to open the preprocessd fMRI dataset in the subject's native space ("denoised_func_data_noaggr.nii"), before applying spatial transformations with the following command:
applywarp -i denoised_func_data_nonaggr.nii -r standard.nii --premat=example_func2highres.mat -w highres2standard_warp.nii -v -o denoised_func_data_standard.nii
Am I missing something?
Originally posted by Alfonso Nieto-Castanon:
Dear Giuseppe,
That error seems to indicate some general/unspecified problem with the denoised_func_data_standard.nii file. Can you please check whether you are able to open/view that file in SPM or some other software? (e.g. use
spm_check_registration 'C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii'
Best
Alfonso
Originally posted by Giuseppe Pontillo:
That error seems to indicate some general/unspecified problem with the denoised_func_data_standard.nii file. Can you please check whether you are able to open/view that file in SPM or some other software? (e.g. use
spm_check_registration 'C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii'
Best
Alfonso
Originally posted by Giuseppe Pontillo:
Dear CONN experts,
I'm trying to import preprocessed rs-fMRI data into CONN for subsequent analyses.
The data have been preprocessed according to FSL's melodic pipeline (which included motion correction with mcflirt, topup-based EPI distortion correction, high-pass filtering and no slice-timing correction since these are multiband, HCP-style fMRI data) followed by ICA-based denoising using FSL's ICA-AROMA.
I managed to import MNI-space structural data, as well as segmented tissue maps, motion parameters derived from mcflirt and outliers estimated by fsl_motion_outliers for the subsequent step.
Unfortunately, when trying to import precprocessed fMRI data as the primary functional dataset, I get the following error:
ERROR DESCRIPTION:
Error using conn_menu>conn_spm_read_vols (line 1091)
Error reading file C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii. File may have been modified or relocated. Please load file again
Error in conn_menu (line 656)
[temp,volhdr]=conn_spm_read_vols(title(n));
Error in conn (line 2049)
conn_menu('updateimage',CONN_h.menus.m_setup_00{5},cfile{3});
Error in conn_filesearchtool (line 222)
if length(h.callback)>1, feval(h.callback{1},h.callback{2:end},names); else, feval(h.callback{1},names); end
Am I missing something?
Once I manage to import the data, my idea is to go through functional smoothing and denoising before statistical analyses, do you suggest any additional step?
Thanks in advance for your precious help,
Giuseppe
I'm trying to import preprocessed rs-fMRI data into CONN for subsequent analyses.
The data have been preprocessed according to FSL's melodic pipeline (which included motion correction with mcflirt, topup-based EPI distortion correction, high-pass filtering and no slice-timing correction since these are multiband, HCP-style fMRI data) followed by ICA-based denoising using FSL's ICA-AROMA.
I managed to import MNI-space structural data, as well as segmented tissue maps, motion parameters derived from mcflirt and outliers estimated by fsl_motion_outliers for the subsequent step.
Unfortunately, when trying to import precprocessed fMRI data as the primary functional dataset, I get the following error:
ERROR DESCRIPTION:
Error using conn_menu>conn_spm_read_vols (line 1091)
Error reading file C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii. File may have been modified or relocated. Please load file again
Error in conn_menu (line 656)
[temp,volhdr]=conn_spm_read_vols(title(n));
Error in conn (line 2049)
conn_menu('updateimage',CONN_h.menus.m_setup_00{5},cfile{3});
Error in conn_filesearchtool (line 222)
if length(h.callback)>1, feval(h.callback{1},h.callback{2:end},names); else, feval(h.callback{1},names); end
Am I missing something?
Once I manage to import the data, my idea is to go through functional smoothing and denoising before statistical analyses, do you suggest any additional step?
Thanks in advance for your precious help,
Giuseppe
Oct 13, 2020 05:10 AM | stity - University of Southern California
RE: FSL preprocessing + conn
Hi,
I encounter the same issue with a 600 time point pre processed 4-D file, but my files are already in 16int
load_nii('swradata.nii')
ans =
struct with fields:
best
Stephanie
Originally posted by Alfonso Nieto-Castanon:
I encounter the same issue with a 600 time point pre processed 4-D file, but my files are already in 16int
load_nii('swradata.nii')
ans =
struct with fields:
best
Stephanie
Originally posted by Alfonso Nieto-Castanon:
Hi
Giuseppe,
A couple of "easier" things to try first would be to: a) restart your computer (if the file has been locked by some other concurrent Windows process this should unlock it); and/or b) copy the file to a different folder (same reasoning as before). If none of this works and the issue is really related to the file size, another possibility would be to resample the file using int16 encoding (dt = [4 0]), which should result in a file of approximately 1Gb (assuming 600 timepoints and 2mm isotropic voxels)
Hope this helps
Alfonso
Originally posted by Giuseppe Pontillo:
A couple of "easier" things to try first would be to: a) restart your computer (if the file has been locked by some other concurrent Windows process this should unlock it); and/or b) copy the file to a different folder (same reasoning as before). If none of this works and the issue is really related to the file size, another possibility would be to resample the file using int16 encoding (dt = [4 0]), which should result in a file of approximately 1Gb (assuming 600 timepoints and 2mm isotropic voxels)
Hope this helps
Alfonso
Originally posted by Giuseppe Pontillo:
I think I figured
it out: it was a file size issue https://en.wikibooks.org/wiki/SPM/Workin...
The 4D fMRI dataset is really large (600 timepoints, about 2 GB).
Do you have any solutions (I'm working on a Windows 64-bit, 32GB RAM PC)?
Originally posted by Giuseppe Pontillo:
The 4D fMRI dataset is really large (600 timepoints, about 2 GB).
Do you have any solutions (I'm working on a Windows 64-bit, 32GB RAM PC)?
Originally posted by Giuseppe Pontillo:
Dear
Alfonso,
thank you so much for your feedback.
Indeed, while I'm able to open/view that file in mricron or fsleyes, I cannot view it in SPM.
This is the error I get when trying to display the file in SPM:
Cannot access file "C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii".
Error using spm_slice_vol
Cant map view of file. It may be locked by another program.
Strangely enough, SPM is perfectly able to open the preprocessd fMRI dataset in the subject's native space ("denoised_func_data_noaggr.nii"), before applying spatial transformations with the following command:
applywarp -i denoised_func_data_nonaggr.nii -r standard.nii --premat=example_func2highres.mat -w highres2standard_warp.nii -v -o denoised_func_data_standard.nii
Am I missing something?
Originally posted by Alfonso Nieto-Castanon:
thank you so much for your feedback.
Indeed, while I'm able to open/view that file in mricron or fsleyes, I cannot view it in SPM.
This is the error I get when trying to display the file in SPM:
Cannot access file "C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii".
Error using spm_slice_vol
Cant map view of file. It may be locked by another program.
Strangely enough, SPM is perfectly able to open the preprocessd fMRI dataset in the subject's native space ("denoised_func_data_noaggr.nii"), before applying spatial transformations with the following command:
applywarp -i denoised_func_data_nonaggr.nii -r standard.nii --premat=example_func2highres.mat -w highres2standard_warp.nii -v -o denoised_func_data_standard.nii
Am I missing something?
Originally posted by Alfonso Nieto-Castanon:
Dear Giuseppe,
That error seems to indicate some general/unspecified problem with the denoised_func_data_standard.nii file. Can you please check whether you are able to open/view that file in SPM or some other software? (e.g. use
spm_check_registration 'C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii'
Best
Alfonso
Originally posted by Giuseppe Pontillo:
That error seems to indicate some general/unspecified problem with the denoised_func_data_standard.nii file. Can you please check whether you are able to open/view that file in SPM or some other software? (e.g. use
spm_check_registration 'C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii'
Best
Alfonso
Originally posted by Giuseppe Pontillo:
Dear CONN experts,
I'm trying to import preprocessed rs-fMRI data into CONN for subsequent analyses.
The data have been preprocessed according to FSL's melodic pipeline (which included motion correction with mcflirt, topup-based EPI distortion correction, high-pass filtering and no slice-timing correction since these are multiband, HCP-style fMRI data) followed by ICA-based denoising using FSL's ICA-AROMA.
I managed to import MNI-space structural data, as well as segmented tissue maps, motion parameters derived from mcflirt and outliers estimated by fsl_motion_outliers for the subsequent step.
Unfortunately, when trying to import precprocessed fMRI data as the primary functional dataset, I get the following error:
ERROR DESCRIPTION:
Error using conn_menu>conn_spm_read_vols (line 1091)
Error reading file C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii. File may have been modified or relocated. Please load file again
Error in conn_menu (line 656)
[temp,volhdr]=conn_spm_read_vols(title(n));
Error in conn (line 2049)
conn_menu('updateimage',CONN_h.menus.m_setup_00{5},cfile{3});
Error in conn_filesearchtool (line 222)
if length(h.callback)>1, feval(h.callback{1},h.callback{2:end},names); else, feval(h.callback{1},names); end
Am I missing something?
Once I manage to import the data, my idea is to go through functional smoothing and denoising before statistical analyses, do you suggest any additional step?
Thanks in advance for your precious help,
Giuseppe
I'm trying to import preprocessed rs-fMRI data into CONN for subsequent analyses.
The data have been preprocessed according to FSL's melodic pipeline (which included motion correction with mcflirt, topup-based EPI distortion correction, high-pass filtering and no slice-timing correction since these are multiband, HCP-style fMRI data) followed by ICA-based denoising using FSL's ICA-AROMA.
I managed to import MNI-space structural data, as well as segmented tissue maps, motion parameters derived from mcflirt and outliers estimated by fsl_motion_outliers for the subsequent step.
Unfortunately, when trying to import precprocessed fMRI data as the primary functional dataset, I get the following error:
ERROR DESCRIPTION:
Error using conn_menu>conn_spm_read_vols (line 1091)
Error reading file C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii. File may have been modified or relocated. Please load file again
Error in conn_menu (line 656)
[temp,volhdr]=conn_spm_read_vols(title(n));
Error in conn (line 2049)
conn_menu('updateimage',CONN_h.menus.m_setup_00{5},cfile{3});
Error in conn_filesearchtool (line 222)
if length(h.callback)>1, feval(h.callback{1},h.callback{2:end},names); else, feval(h.callback{1},names); end
Am I missing something?
Once I manage to import the data, my idea is to go through functional smoothing and denoising before statistical analyses, do you suggest any additional step?
Thanks in advance for your precious help,
Giuseppe