External Email - Use Caution Mean correlation values to the seed from activations of a pcc.mgh map from each individual subject.
On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > mean over what? a parcellation? an activation cluster? > > On 10/31/2019 3:15 PM, Amrita Bedi wrote: > > External Email - Use Caution > Thank you Dr Greve, that issue is resolved. > > 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. < > dgr...@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: *abedi...@citymail.cuny.edu <mailto:abedi...@citymail.cuny.edu>* >> > <abedi...@citymail.cuny.edu <mailto:abedi...@citymail.cuny.edu>> >> > Date: Thursday, October 31, 2019 >> > Subject: Fw: glm error >> > To: Amrita Bedi <amibedi...@gmail.com <mailto:amibedi...@gmail.com>> >> > >> > >> > >> > >> > Amrita Bedi >> > /Biomedical Engineering - Class of 2018/ >> > /The City College of New York - CUNY/ >> > >> > ------------------------------------------------------------ >> ------------ >> > *From:* abedi...@citymail.cuny.edu <mailto:abedi...@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_1to >> 547_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_1to >> 547_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_1t >> o547_TR3/FSFAST/4D_VOLUME_OUTPUT.lh.nii.gz >> > logyflag 0 >> > usedti 0 >> > labelmask >> > /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_1t >> o547_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. >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >
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