I do have another question. I’m now trying to extract mean correlation values to the seed from each individual subject and not sure how to go about this.

On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

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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