I think you have a non-standard directory structure. FS is expecting something like $SUBJECTS_DIR/subject1 but it looks like you have the FS results in $SUBJECTS_DIR/subject1/freesurfer You have to use the FS structure or else it will generate an error doug
On 07/20/2015 03:14 PM, David C. Zhu wrote: > 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 . If the e-mail was sent to you in > error but does not contain patient information, please contact the sender and > properly dispose of the e-mail. > > > _______________________________________________ > 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
