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
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