Dear Doug, I was away a while and missed your email.
I have not resolved this issue yet. Could you please help? Thanks. David -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, June 29, 2015 6:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] help on mris_preproc Hi David, did you resolve this? doug On 06/12/2015 04:56 PM, David C. Zhu wrote: > > Hi Doug, > > Thanks. > > I can see that the "mris_preproc" command reads the header information > in "register.dat". > > I set the "." as the $SUBJECTS_DIR, and thus it seems that > "mris_preproc" cannot locate the path. Is there a way to fix this? > > David > > Here is the (part of) output: > > ------ > > end > > while ( $#argv != 0 ) > > while ( 27 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --iv > > shift > > switch ( $flag ) > > switch ( --iv ) > > case "--ivp": > > case --ivp: > > if ( $#argv < 2 ) goto arg2err ; > > if ( 26 < 2 ) goto arg2err > > set ivp = $argv[1] ; shift ; > > set ivp = S02520110927_Free/sum_all_norm_IRF_EA.nii > > shift > > if ( ! -e $ivp ) then > > if ( ! -e S02520110927_Free/sum_all_norm_IRF_EA.nii ) then > > set irp = $argv[1] ; shift ; > > set irp = S02520110927_Free/register.dat > > shift > > if ( ! -e "$irp" ) then > > if ( ! -e S02520110927_Free/register.dat ) then > > set ivplist = ( $ivplist $ivp ) ; > > set ivplist = ( S00720110927_Free/sum_all_norm_IRF_EA.nii > S01420110908_Free/sum_all_norm_IRF_EA.nii > S01520110811_Free/sum_all_norm_IRF_EA.nii > S02520110927_Free/sum_all_norm_IRF_EA.nii ) > > set irplist = ( $irplist $irp ) ; > > set irplist = ( S00720110927_Free/register.dat > S01420110908_Free/register.dat S01520110811_Free/register.dat > S02520110927_Free/register.dat ) > > set subj = `head -1 $irp` ; > > set subj = `head -1 $irp` > > head -1 S02520110927_Free/register.dat > > set subjlist = ( $subjlist $subj ) ; > > set subjlist = ( freesurfer freesurfer freesurfer freesurfer ) > > set srcvol = 1 ; > > set srcvol = 1 > > breaksw > > breaksw > > end > > end > > ... > > ... > > ... > > if ( 0 == 0 && 1 == 0 && 0 == 0 ) then if ( $srcsurf && $srcvol ) then > if ( 0 && 1 ) then if ( $srcsurf && $#projfrac != 0 ) then if ( 0 && 0 > != 0 ) then if ( $catmean && $catstd ) then if ( 0 && 0 ) then if ( > $#meas && $#isplist ) then if ( 0 && 0 ) then if ( $MeasIn && $CacheIn > ) then if ( 0 && 0 ) then if ( $#ivplist != 0 ) then if ( 12 != 0 ) > then if ( $#ivplist != $#subjlist ) then if ( 12 != 12 ) then endif > endif if ( $#isplist != 0 ) then if ( 0 != 0 ) then if ( $paireddiff > && ! $DoXHemi ) then if ( 0 && ! 0 ) then > > if ( ! -e $SUBJECTS_DIR ) then > if ( ! -e . ) then > > > if ( $DoXHemi ) then > if ( 0 ) then > > echo "nsubjects = $#subjlist" ; > echo nsubjects = 12 > nsubjects = 12 > @ nthsubj = 1 ; > @ nthsubj = 1 > foreach subj ( $subjlist ) > foreach subj ( freesurfer freesurfer freesurfer freesurfer freesurfer > freesurfer freesurfer freesurfer freesurfer freesurfer freesurfer > freesurfer ) set subjpath = $SUBJECTS_DIR/$subj set subjpath = > ./freesurfer if ( ! -e $subjpath ) then if ( ! -e ./freesurfer ) then > echo "ERROR: cannot find $subjpath" > echo ERROR: cannot find ./freesurfer > ERROR: cannot find ./freesurfer > exit 1 ; > exit 1 > > *From:*freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas > Greve > *Sent:* Friday, June 12, 2015 3:51 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] help on mris_preproc > > Can you run the 2nd command with --debug as the first option and send > the terminal output? > doug > > On 6/12/15 12:09 PM, David C. Zhu wrote: > > Dear FreeSurfer experts: > > I have been using FreeSurfer for segmentation and for volumetric > analyses. I want to give a try to use it for surface-based fMRI > analyses. > > I encountered some issues with mris_preproc to assemble IRF > results to the fsaverage surface. Please advise on how to resolve > these issues. > > Here is what I did: > > After finishing "recon-all" on each subject, I ran this following > on each subject. > > bbregister --mov reg_cat_TSall_before_blur.nii --bold --s > freesurfer --init-fsl --lta register.lta > > "reg_cat_TSall_before_blur.nii" is the EPI fMRI time series > assembled together. > > Then I calculated the IRF percent signal changes for different > conditions. "sum_all_norm_IRF_EA.nii" is for one condition. > > Now I want to assemble the "sum_all_norm_IRF_EA.nii" from each > subject and put them on the fsaverage surface. I got the following > errors: > > mris_preproc --hemi rh --o rh.fsaverage.sumEA.mgh \ > > --iv S00720110927_Free/sum_all_norm_IRF_EA.nii > S00720110927_Free/register.lta \ > > --iv S01420110908_Free/sum_all_norm_IRF_EA.nii > S01420110908_Free/register.lta \ > > --iv S01520110811_Free/sum_all_norm_IRF_EA.nii > S01520110811_Free/register.lta \ > > --iv S02520110927_Free/sum_all_norm_IRF_EA.nii > S02520110927_Free/register.lta \ > > --iv S02720111028_Free/sum_all_norm_IRF_EA.nii > S02720111028_Free/register.lta \ > > --iv S02820111107_Free/sum_all_norm_IRF_EA.nii > S02820111107_Free/register.lta \ > > --iv S02920111108_Free/sum_all_norm_IRF_EA.nii > S02920111108_Free/register.lta \ > > --iv S03020120703_Free/sum_all_norm_IRF_EA.nii > S03020120703_Free/register.lta \ > > --iv S03120120726_Free/sum_all_norm_IRF_EA.nii > S03120120726_Free/register.lta \ > > --iv S03620120727_Free/sum_all_norm_IRF_EA.nii > S03620120727_Free/register.lta \ > > --iv S03720120809_Free/sum_all_norm_IRF_EA.nii > S03720120809_Free/register.lta \ > > --iv S03920120807_Free/sum_all_norm_IRF_EA.nii > S03920120807_Free/register.lta > > ERROR: number of input volumes (12) does not equal number of > subjects (48) > > mris_preproc --hemi rh --o rh.fsaverage.sumEA.mgh \ > > --iv S00720110927_Free/sum_all_norm_IRF_EA.nii > S00720110927_Free/register.dat \ > > --iv S01420110908_Free/sum_all_norm_IRF_EA.nii > S01420110908_Free/register.dat \ > > --iv S01520110811_Free/sum_all_norm_IRF_EA.nii > S01520110811_Free/register.dat \ > > --iv S02520110927_Free/sum_all_norm_IRF_EA.nii > S02520110927_Free/register.dat \ > > --iv S02720111028_Free/sum_all_norm_IRF_EA.nii > S02720111028_Free/register.dat \ > > --iv S02820111107_Free/sum_all_norm_IRF_EA.nii > S02820111107_Free/register.dat \ > > --iv S02920111108_Free/sum_all_norm_IRF_EA.nii > S02920111108_Free/register.dat \ > > --iv S03020120703_Free/sum_all_norm_IRF_EA.nii > S03020120703_Free/register.dat \ > > --iv S03120120726_Free/sum_all_norm_IRF_EA.nii > S03120120726_Free/register.dat \ > > --iv S03620120727_Free/sum_all_norm_IRF_EA.nii > S03620120727_Free/register.dat \ > > --iv S03720120809_Free/sum_all_norm_IRF_EA.nii > S03720120809_Free/register.dat \ > > --iv S03920120807_Free/sum_all_norm_IRF_EA.nii > S03920120807_Free/register.dat > > nsubjects = 12 > > ERROR: cannot find ./freesurfer > > Under each subject directory, for example, "S00720110927_Free", I > have the following data structure (The "freesurfer" storing the > "recon-all" FreeSurfer results.): > > circ2:/fmri/PI/liu/rdl_afni/S00720110927_Free> ls > > freesurfer lh.sum_all_norm_IRF_MA.mgh register.dat.mincost > rh.sum_all_norm_IRF_HA.mgh sum_all_norm_IRF_HS.nii > > fsaverage lh.sum_all_norm_IRF_MS.mgh register.dat.param > rh.sum_all_norm_IRF_HS.mgh sum_all_norm_IRF_MA.nii > > lh.EC_average mprage_nudge_RAI.nii.gz > register.dat.sum rh.sum_all_norm_IRF_MA.mgh > sum_all_norm_IRF_MS.nii > > lh.sum_all_norm_IRF_EA.mgh reg_cat_TSall_before_blur.nii > register.lta rh.sum_all_norm_IRF_MS.mgh surfer.log > > lh.sum_all_norm_IRF_ES.mgh register.dat > rh.EC_average sum_all_norm_IRF_EA.nii > > lh.sum_all_norm_IRF_HA.mgh register.dat~ > rh.sum_all_norm_IRF_EA.mgh sum_all_norm_IRF_ES.nii > > lh.sum_all_norm_IRF_HS.mgh register.dat.log > rh.sum_all_norm_IRF_ES.mgh sum_all_norm_IRF_HA.nii > > Thank you. > > David Zhu > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . 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