You are not creating the 4D_VOLUME_OUTPUT.lh.nii.gz file correctly Try mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i */Bold/PCC_Bold1_L/bilat*/pcc.nii.gz
Where you have "bilat*", that should only be one folder
On 10/31/19 12:04 PM, Amrita Bedi wrote:
External Email - Use Caution
---------- Forwarded message ---------- From: *abedi000@citymail.cuny.edu mailto:abedi000@citymail.cuny.edu* <abedi000@citymail.cuny.edu mailto:abedi000@citymail.cuny.edu> Date: Thursday, October 31, 2019 Subject: Fw: glm error To: Amrita Bedi <amibedi273@gmail.com mailto:amibedi273@gmail.com>
Amrita Bedi /Biomedical Engineering - Class of 2018/ /The City College of New York - CUNY/
*From:* abedi000@citymail.cuny.edu mailto:abedi000@citymail.cuny.edu *Sent:* Thursday, October 31, 2019 12:02 PM *To:* Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu <Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> *Subject:* glm error Hello Freesurfer developers,
I ran a seed based resting stage functional analysis for 287 subjects using the isthmus of the cingulate as a seed and now have pcc.nii.gz files in each individual subject folder. I concatenated these pcc files and am trying to run an osgm but get the following error: ERROR: DOF = 0 The commands i ran for concatenating and glm are: for l in `cat sessidBOLD2`; do mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i $l/Bold/PCC_Bold1_L/bilat*/pcc.nii.gz; done
mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh --cortex --label /run/media/amritabedilocal/DATA/Amrita/2389/abedi /FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir all_subjects_lh_ic_pcc.TR3.glmdir
The mriglmfit.log gave me the following:
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/FSFAST cmdline mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh --cortex --label /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir all_subjects_lh_ic_pcc.TR3.glmdir sysname Linux hostname imaging5.vaboston.lan machine x86_64 user root FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/FSFAST/4D_VOLUME_OUTPUT.lh.nii.gz logyflag 0 usedti 0 labelmask /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label maskinv 0 glmdir all_subjects_lh_ic_pcc.TR3.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0
Thank you for your help.
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