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help > RE: Field mapping correction
Feb 20, 2019 04:02 PM | Dayana Hayek - Charite Universität Medizin Berlin
RE: Field mapping correction
Well, I did the common mistake and put
the total readout timing of the field mapping and not the BOLD :)
Now it works perfectly fine!
Thank you so much :)
Best,
Dayana
Originally posted by Alfonso Nieto-Castanon:
Thank you so much :)
Best,
Dayana
Originally posted by Alfonso Nieto-Castanon:
Hi
Dayana,
It could be a problem with the sequence itself, but perhaps most likely it might just be a mis-specification of the acquisition parameters, since those effectively control the scale and directionality of the applied spatial correction. The general tips are:
1) if you see that the correction seems to be doing just the opposite of what it "should" do (e.g something that looked compressed along the phase-encoded direction before the correction, now it looks even more compressed after the correction) then that might indicate an incorrect BLIP direction specification, so simply try again but now switching the BLIP directionality (if you used -1 switch to +1, and viceversa)
2) if you see that the correction seems to go in the correct direction, but either doing too much or too little (e.g. something that looked compressed along the phase-encoded direction before the correction, now it looks too elongated after the correction) that might indicate an incorrect timing information. Double-check your First- and Second- echo time values (these are values specific to your fieldmap sequence, and often vendor-specific) and your EPI total readout time (this is a value specific to your functional sequence). A common mistake here, for example, is to enter the total readout time of your fieldmap acquisition instead of the value of your actual EPI / functional-data acquisition, as those are often widely different values. If in doubt, check the original DICOM files to look for those values, and/or use dcm2niix to attempt to extract that information automatically and save it to sidecar .json files (which then CONN can read).
Hope this helps
Alfonso
Originally posted by Dayana Hayek:
It could be a problem with the sequence itself, but perhaps most likely it might just be a mis-specification of the acquisition parameters, since those effectively control the scale and directionality of the applied spatial correction. The general tips are:
1) if you see that the correction seems to be doing just the opposite of what it "should" do (e.g something that looked compressed along the phase-encoded direction before the correction, now it looks even more compressed after the correction) then that might indicate an incorrect BLIP direction specification, so simply try again but now switching the BLIP directionality (if you used -1 switch to +1, and viceversa)
2) if you see that the correction seems to go in the correct direction, but either doing too much or too little (e.g. something that looked compressed along the phase-encoded direction before the correction, now it looks too elongated after the correction) that might indicate an incorrect timing information. Double-check your First- and Second- echo time values (these are values specific to your fieldmap sequence, and often vendor-specific) and your EPI total readout time (this is a value specific to your functional sequence). A common mistake here, for example, is to enter the total readout time of your fieldmap acquisition instead of the value of your actual EPI / functional-data acquisition, as those are often widely different values. If in doubt, check the original DICOM files to look for those values, and/or use dcm2niix to attempt to extract that information automatically and save it to sidecar .json files (which then CONN can read).
Hope this helps
Alfonso
Originally posted by Dayana Hayek:
Hi
Alfonso,
Thank you so much!
I ran it and it worked. However, the results look weird. From my understanding of field mapping correction, is to correct for distortions to avoid drop out or signal loss that is most prevalent in the frontal lobe. So ideally, after field mapping correction, frontal lobes should look better and not worse. But in my results, as if frontal lobe is trimmed (attached pic). Could it be a problem of the sequence we acquired? or is there any other technical reason?
Thanks in advance for your support,
Best,
Dayana
Originally posted by Alfonso Nieto-Castanon:
Thank you so much!
I ran it and it worked. However, the results look weird. From my understanding of field mapping correction, is to correct for distortions to avoid drop out or signal loss that is most prevalent in the frontal lobe. So ideally, after field mapping correction, frontal lobes should look better and not worse. But in my results, as if frontal lobe is trimmed (attached pic). Could it be a problem of the sequence we acquired? or is there any other technical reason?
Thanks in advance for your support,
Best,
Dayana
Originally posted by Alfonso Nieto-Castanon:
Hi
Dayana,
Sorry about that, the error message was a bug in the code which was not handling your scenario correctly (you seem to have a single 4d volume containing two magnitude images, and another 3d volume containing the phasediff image). Please try the attached patch and let me know if you still run into any issues (note: this patch is for release 18b, to install it simply copy the attached file to the conn distribution folder overwriting the file with the same name there)
Regarding the image seemingly changing in the display when selecting only the magnitude volume and the magnitude+phase volumes, that is perfectly fine, it is just an issue with the intensity scaling of the display changing between the two displays (the display in the right is scaled in a way that shows both positive and negative values, while the display in the left is scaled differently since all values shown are positive).
Last, regarding entering these files without using the GUI, you could perhaps use something like the following:
nses = 1;
for nsub = 1:numel(filenames) conn_set_functional(nsub,nses,'fmap',filenames{nsub}); end
where the variables filenames contains the list of the file pairs for each subject, so it should look something like:
filenames = { ...
{'/data/subject1/magnitude.nii','/data/subject1/phase.nii'} ...
{'/data/subject2/magnitude.nii','/data/subject2/phase.nii'} ...
{'/data/subject3/magnitude.nii','/data/subject3/phase.nii'} ...
... etc.
};
Hope this helps
Alfonso
Originally posted by Dayana Hayek:
Sorry about that, the error message was a bug in the code which was not handling your scenario correctly (you seem to have a single 4d volume containing two magnitude images, and another 3d volume containing the phasediff image). Please try the attached patch and let me know if you still run into any issues (note: this patch is for release 18b, to install it simply copy the attached file to the conn distribution folder overwriting the file with the same name there)
Regarding the image seemingly changing in the display when selecting only the magnitude volume and the magnitude+phase volumes, that is perfectly fine, it is just an issue with the intensity scaling of the display changing between the two displays (the display in the right is scaled in a way that shows both positive and negative values, while the display in the left is scaled differently since all values shown are positive).
Last, regarding entering these files without using the GUI, you could perhaps use something like the following:
nses = 1;
for nsub = 1:numel(filenames) conn_set_functional(nsub,nses,'fmap',filenames{nsub}); end
where the variables filenames contains the list of the file pairs for each subject, so it should look something like:
filenames = { ...
{'/data/subject1/magnitude.nii','/data/subject1/phase.nii'} ...
{'/data/subject2/magnitude.nii','/data/subject2/phase.nii'} ...
{'/data/subject3/magnitude.nii','/data/subject3/phase.nii'} ...
... etc.
};
Hope this helps
Alfonso
Originally posted by Dayana Hayek:
Hi Alfonso,
Thank you so much for the quick reply!
I did exactly what you have said, but I have an error "Error using FieldMap_create (line 139); Funny number of input fieldmap images".
What I found also weird (attached pic) is that when I load the magnitude alone, it appears ok (left side of the pic) and when I load both magnitude and phase, the image changes (right side of the pic). I am not sure what is happening?
One last question, is it possible to load two image for each subject but not manually, for multiple subject? I used the ALT-select option to load functional and structural data for multiple subject, but it doesn't seem to work when there are two file for each subject.
Thanks,
Regards,
Dayana
Thank you so much for the quick reply!
I did exactly what you have said, but I have an error "Error using FieldMap_create (line 139); Funny number of input fieldmap images".
What I found also weird (attached pic) is that when I load the magnitude alone, it appears ok (left side of the pic) and when I load both magnitude and phase, the image changes (right side of the pic). I am not sure what is happening?
One last question, is it possible to load two image for each subject but not manually, for multiple subject? I used the ALT-select option to load functional and structural data for multiple subject, but it doesn't seem to work when there are two file for each subject.
Thanks,
Regards,
Dayana
Threaded View
| Title | Author | Date |
|---|---|---|
| Dayana Hayek | Feb 13, 2019 | |
| jothini | Mar 1, 2024 | |
| Yi Ding | Nov 20, 2020 | |
| Dayana Hayek | Mar 6, 2019 | |
| boris | Feb 22, 2019 | |
| Alfonso Nieto-Castanon | Feb 27, 2019 | |
| boris | Feb 27, 2019 | |
| Zhaoxia Qin | Feb 22, 2019 | |
| Alfonso Nieto-Castanon | Feb 14, 2019 | |
| Dayana Hayek | Feb 15, 2019 | |
| Alfonso Nieto-Castanon | Feb 15, 2019 | |
| Juan Dominguez | Feb 27, 2019 | |
| Alfonso Nieto-Castanon | Feb 27, 2019 | |
| Dayana Hayek | Feb 20, 2019 | |
| Alfonso Nieto-Castanon | Feb 20, 2019 | |
| Dayana Hayek | Feb 20, 2019 | |
| Victoria Okuneye | Feb 15, 2019 | |
| Alfonso Nieto-Castanon | Feb 15, 2019 | |
| madeleine | Oct 15, 2020 | |
| Alfonso Nieto-Castanon | Oct 15, 2020 | |
| madeleine | Oct 16, 2020 | |
| madeleine | Oct 19, 2020 | |