NITRC PESTICA & SLOMOCO: physio and motion correction tools Forum: open-discussion

Coregistration to MNI-template - adjusted FOV

mthalhammer — Tue, 07 Jun 2022 6:40:57 GMT

Dear Pestica-community,

I had a problems regarding the coregistration of my EPI to the MNI-template recently when using PESTICA, version 5. The Pestica [url=https://www.nitrc.org/frs/download.php/4774/pestica_tutorial_v2.pdf]tutorial[/url] (version 2, pages 22 and 23) states that one should check the coregistration to MNI EPI template while making "sure resp_PESTICA.nii and card_PESTICA.nii line up over your data".

I have worked on two different datasets run within the same patients and MRI run:
1) EPI of wholebrain in low resolution (3*3*3mm) and
2) EPI of reduced FOV covering only the brainstem.

When checking the coregistration of dataset 1) in fsleyes, everything looks fine. However, dataset 2) with the reduced FOV seems not aligned that well, even though my final results look promising. So, I was wondering how Pestica uses card_PESTICA and resp_PESTICA in further processing and whether I could/should change something in the script to fix this (for example adding 3dAllineate as suggested in [url=https://www.nitrc.org/forum/forum.php?thread_id=4107&forum_id=1456]this [/url]post).

Best, Melissa Thalhammer

RE: Ubuntu Update causing errors

Marlene Tahedl — Wed, 08 Dec 2021 21:17:35 GMT

Hi!

I realize this was posted quite a while ago, but right now I'm encountering the exact same problem with SLOMOCO (using a Mac, OSX Big Sur 11.1). Has anybody found a solution to this problem by now?

Any help would be appreciated :)

Thanks!

RE: afni_matlab problem

Marlene Tahedl — Wed, 08 Dec 2021 18:04:39 GMT

I had the same problem after upgrading to MATLAB 2021b. This trick solved the problem. Thanks a lot!

Lacking A TAXIS OFFSET

hmri — Thu, 14 Nov 2019 17:34:59 GMT

Hello,

I just downloaded this program. I am trying to run a BOLD scan through this, but it turns out, in BrickInfo.m, when I try to display BRIKinfo, there is no TAXIS_OFFSETS section for the program to grab and store. This is causing the program to crash. Is there anything that I can do?

Best regards,
Jimi

Multi-band acceleration factor

davidb — Tue, 20 Aug 2019 9:29:05 GMT

Hi all,

I was wondering if the slice_timing matlab functions also take into account the multi-band acceleration factor?

Many thanks

David

RE: a tip for matlab error in csh/tcsh envirn

davidb — Wed, 19 Jun 2019 11:38:02 GMT

[color=#000000]Hi,[/color]

Would it be possible to know what exactly should be added to the setup_pestica.sh file without modifying the .bashrc file so that the program can use matlab?

Many thanks for your help

Best

David

[i]Originally posted by Wanyong Shin:[/i][quote][color=#000000]Thanks, Hang Joon.[/color]

[color=#000000]You can modify setup_pestica.sh to modify path and "MATLABLINE" [/color]

-Wanyong

[i]Originally posted by Hang Joon Jo:[/i][quote]I have no idea whether it's discussed before.

If you run pestica in csh/tcsh environment, "no matlab command" error might be shown up in particular systems.

I found a workaround in that case - "Add matlab path and alias in .bashrc" even you don't use bash. In my case:

export PATH=$PATH:/Applications/MATLAB_R2015a.app/bin
alias matlab='/Applications/MATLAB_R2015a.app/bin/matlab -nodesktop'

Hope this help.

- H[/quote][/quote]

Ubuntu Update causing errors

David Cunningham — Wed, 03 Apr 2019 15:41:21 GMT

Hello,

I recently updated ubuntu to 18.04.2.

Since doing this I've been receiving 3drefit errors while using slicemoco_newalgorithm.sh. Specifically, the error reads:

mri_read_ascii: couldn't open file 242 31 77002 -999 -999 -999 -999 -999

I've attached the full output in a text file.

Has anyone run into a similar problem?

Thanks

a tip for background intensity correction after pestica

Hang Joon Jo — Thu, 14 Feb 2019 6:05:56 GMT

Hi Folks,

PESTICA processes could increase the background intensity, and there might be a trouble to perform further processes (i.e. getting a wrong brain mask from the output irfretroicor file during afni_proc.py process).

Few AFNI command lines can correct the background intensity problem:

# pick the time course intensities at voxel index 1 1 1
3dmaskdump -quiet -noijk -ibox 1 1 1 [output irfretroicor file here]+orig. > temp.1D
# sort the intensities
1dTsort temp.1D\' > tempsort.1D

# For tcsh, get the minimum number of background, but mostly identical to each other.
set mm = '1dcat tempsort.1D'{0}''

# subtract the minimum background intensity across time points
3dcalc -a pb01.irfretroicor+orig. -expr 'a-'${mm}'' -prefix irfretroicor_bg_fix

I hope this helps.

H

sharing a solution to fixing errors running slomoco

Yuqi Liu — Thu, 12 Apr 2018 17:31:11 GMT

I recently started using pestica4 and kept getting errors running slicemoco_newalgorithm.sh. After some inspections I fixed it, and want to share with other uses.

So after typing slicemoco_newalgorithm.sh -d , I got errors below during secondorder motor correction:

----------------------------------------------------
----------------------------------------------------
finished slicewise in-plane motion correction

Exiting
Running Secondorder Motion Correction using SLOMOCO output
matlab -nodesktop -nosplash addpath /Users/yuqiliu/Downloads/pestica4/slomoco; addpath /Users/yuqiliu/Downloads/pestica4/afni_matlab; addpath /Users/yuqiliu/Downloads/pestica4/pestica_matlab; slicemoco_newalgorithm_input('tactile_run1.slicemocoxy_afni+orig','tactile_run1.brain+orig','tempslmoco_volslc_alg_vol_tactile_run1.slicemocoxy_afni/motion.wholevol_zt'); exit;
< M A T L A B (R) >
Copyright 1984-2016 The MathWorks, Inc.
R2016b (9.1.0.441655) 64-bit (maci64)
September 7, 2016
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
>> Note: SMS acquisition is applied (MB acc. fac = 6).
[color=#ff0000]Output argument "tranmat_zt" (and maybe others) not assigned during call to[/color]
[color=#ff0000]"convert_1dmat_into_tranmatarray".[/color]
[color=#ff0000]Error in slicemoco_newalgorithm_input (line 25)[/color]
[color=#ff0000]tranmat_zt = convert_1dmat_into_tranmatarray(transmat1d_zt);% tranmat_zt =[/color]
[color=#ff0000]reshape(tranmat_zt,[zmbdim tdim 3 4]); % (v1) debugged[/color]

-----------------------------------------------------------------------------------------------
-----------------------------------------------------------------------------------------------

I went back to functions involved in the error message and figured it the problem was due to the command [b]gawk[/b] not found. Installing gawk solved my problem.

Best,
Yuqi

"out of memory" issue running pestica4

Yuqi Liu — Sat, 07 Apr 2018 15:49:34 GMT

Hi all,

This is a relatively general question and I am wondering if any one has any suggestions. I am implementing pestica4 on an Ubuntu 16.04 system, and I got an error in Stage 3 of run_pestica.sh:

Running Stage 3: Filtering PESTICA estimators, cardiac first, then respiratory

........(omitted)

Range of typical human cardiac rate: 62+-8bpm (range 48-85)
use a buffer of at least 20bpm around the peaks you like for cardiac
*************************************************************
*************************************************************
[color=#ff0000][b]Error using fread[/b][/color]
[color=#ff0000][b]Out of memory. Type HELP MEMORY for your options.[/b][/color]
Error in BrikLoad (line 651)
V = fread(fidBRIK, (Info.DATASET_DIMENSIONS(1) .* Info.DATASET_DIMENSIONS(2) .*
Info.DATASET_DIMENSIONS(3) .* Info.DATASET_RANK(2)) , [Opt.OutPrecision,typestr]);
Error in view_and_correct_estimator (line 5)
[err, ima, ainfo, ErrMessage]=BrikLoad(ep2d_filename, Opt);

Has anyone had similar issues and any suggestions on how to work this around?

Thank you!
Yuqi