Freesurfer May 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
219 discussions

R: Re: R: Re: selxavg3-sess error
by stdp82＠virgilio.it 16 May '17

16 May '17

Rerunning it is ok ----Messaggio originale---- Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> Data: 16-mag-2017 18.21 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: selxavg3-sess error Does this file exist ? /Applications/freesurfer/subjects/fMRI/subj067_GROUP/001/masks/brain.e3.nii.gz You can try deleting the /Applications/freesurfer/subjects/fMRI/subj067_GROUP/001/masks folder and re-running. On 5/16/17 11:53 AM, stdp82(a)virgilio.it wrote: selxavg3-sess -s subj067_GROUP -a fc.lamgseed.surf.lh -debug set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return foreach grp ( $grpdefs ) foreach grp ( ) goto check_params ; goto check_params if ( $#SessList == 0 ) then if ( 1 == 0 ) then if ( $#SearchPathList == 0 ) then if ( 0 == 0 ) then set SearchPathList = "." ; set SearchPathList = . endif endif goto check_params_return ; goto check_params_return set UniqueList = ( ) ; set UniqueList = ( ) foreach d ( $SearchPathList ) foreach d ( . ) if ( ! -e $d ) then if ( ! -e . ) then set IsUnique = 1 ; set IsUnique = 1 foreach u ( $UniqueList ) foreach u ( ) if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ; if ( 1 ) set UniqueList = ( . ) set UniqueList = ( . ) end end set SearchPathList = ( $UniqueList ) ; set SearchPathList = ( . ) set errs = 0 ; set errs = 0 set SessPath = ( ) ; set SessPath = ( ) foreach sess ( $SessList ) foreach sess ( subj067_GROUP ) set tmp = ( ) ; set tmp = ( ) foreach d ( $SearchPathList ) foreach d ( . ) set stst = $d/$sess set stst = ./subj067_GROUP if ( -d $stst ) then if ( -d ./subj067_GROUP ) then if ( ! -r $stst ) then if ( ! -r ./subj067_GROUP ) then pushd $stst > /dev/null ; pushd ./subj067_GROUP set tmp = ( $tmp `$PWDCMD` ) ; set tmp = ( `$PWDCMD` ) pwd popd > /dev/null ; popd endif endif end end set nfound = ( $#tmp ) ; set nfound = ( 1 ) if ( $nfound == 0 ) then if ( 1 == 0 ) then if ( $nfound > 1 ) then if ( 1 > 1 ) then set SessPath = ( $SessPath $tmp ) ; set SessPath = ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP ) end end set UniqueList = ( ) ; set UniqueList = ( ) foreach s ( $SessPath ) foreach s ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP ) set IsUnique = 1 ; set IsUnique = 1 foreach u ( $UniqueList ) foreach u ( ) if ( ! $IsUnique && ! $AllowRedundant ) then if ( ! 1 && ! 0 ) then set UniqueList = ( $UniqueList $s ) ; set UniqueList = ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP ) endif endif end end echo $SessPath echo /Applications/freesurfer/subjects/fMRI/subj067_GROUP exit $errs ; exit 0 set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params if ( $#SessList == 0 ) then if ( 1 == 0 ) then if ( $#analysis == 0 && $flacfile == 0 ) then if ( 1 == 0 && == 0 ) then if ( $#analysis != 0 ) then if ( 1 != 0 ) then if ( ! -d $analysis ) then if ( ! -d fc.lamgseed.surf.lh ) then if ( ! -e $analysis/analysis.info ) then if ( ! -e fc.lamgseed.surf.lh/analysis.info ) then endif endif if ( $#flacfile != 0 ) then if ( 0 != 0 ) then if ( $perrun && $jkrun ) then if ( 0 && 0 ) then if ( $UseOctave ) then if ( 0 ) then if ( $#DoneFile ) then if ( 0 ) then goto check_params_return ; goto check_params_return set StudyDir = `pwd` ; set StudyDir = `pwd` pwd if ( $#analysis ) then if ( 1 ) then set analysisname = $analysis set analysisname = fc.lamgseed.surf.lh set fsd = `getana -a $analysis -t fsd` ; set fsd = `getana -a $analysis -t fsd` getana -a fc.lamgseed.surf.lh -t fsd set PerSession = `getana -a $analysis -t IsPerSession` set PerSession = `getana -a $analysis -t IsPerSession` getana -a fc.lamgseed.surf.lh -t IsPerSession set IsNative = `getana -a $analysis -t IsNative` set IsNative = `getana -a $analysis -t IsNative` getana -a fc.lamgseed.surf.lh -t IsNative set IsSurface = `getana -a $analysis -t IsSurface` set IsSurface = `getana -a $analysis -t IsSurface` getana -a fc.lamgseed.surf.lh -t IsSurface if ( $IsSurface ) then if ( 1 ) then set subject = `getana -a $analysis -t subject` set subject = `getana -a $analysis -t subject` getana -a fc.lamgseed.surf.lh -t subject set hemi = `getana -a $analysis -t hemi` set hemi = `getana -a $analysis -t hemi` getana -a fc.lamgseed.surf.lh -t hemi echo "Surface data $subject $hemi" echo Surface data fsaverage lh Surface data fsaverage lh endif endif set dt = `getana -a $analysis -t designtype` set dt = `getana -a $analysis -t designtype` getana -a fc.lamgseed.surf.lh -t designtype if ( $dt == "abblocked" ) set RequireContrasts = 0 ; if ( notask == abblocked ) set RequireContrasts = 0 if ( $dt == "retinotopy" ) set RequireContrasts = 0 ; if ( notask == retinotopy ) set RequireContrasts = 0 set contrasts = `getana -a $analysis -t contrasts` set contrasts = `getana -a $analysis -t contrasts` getana -a fc.lamgseed.surf.lh -t contrasts if ( $#contrasts == 0 && $RequireContrasts ) then if ( 1 == 0 && 1 ) then endif endif if ( $#LF == 0 ) then if ( 0 == 0 ) then if ( $nolog ) then if ( 0 ) then if ( $#OutParent == 0 ) then if ( 0 == 0 ) then set logdir = `pwd`/log ; set logdir = `pwd`/log pwd else else mkdir -p $logdir mkdir -p /Applications/freesurfer/subjects/fMRI/log if ( ! -e $logdir ) then if ( ! -e /Applications/freesurfer/subjects/fMRI/log ) then set LF = $logdir/selxavg3-sess-$fsd-$analysis-$DateStr.log set LF = /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log if ( -e $LF ) mv $LF $LF.old if ( -e /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log ) mv /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log.old endif endif endif endif endif endif echo "--------------------------------------------------------------" echo -------------------------------------------------------------- -------------------------------------------------------------- echo "selxavg3-sess logfile is $LF" echo selxavg3-sess logfile is /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log selxavg3-sess logfile is /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log echo "--------------------------------------------------------------" echo -------------------------------------------------------------- -------------------------------------------------------------- echo "selxavg3-sess log file" | tee -a $LF tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log echo selxavg3-sess log file selxavg3-sess log file echo $0 | tee -a $LF tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log echo /Applications/freesurfer/fsfast/bin/selxavg3-sess /Applications/freesurfer/fsfast/bin/selxavg3-sess echo $inputargs | tee -a $LF tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log echo -s subj067_GROUP -a fc.lamgseed.surf.lh -debug -s subj067_GROUP -a fc.lamgseed.surf.lh -debug echo $VERSION | tee -a $LF tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log echo $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ id | tee -a $LF id tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log uid=501(Stefano) gid=20(staff) groups=20(staff),402(com.apple.sharepoint.group.1),12(everyone),61(localaccounts),79(_appserverusr),80(admin),81(_appserveradm),98(_lpadmin),33(_appstore),100(_lpoperator),204(_developer),395(com.apple.access_ftp),398(com.apple.access_screensharing),399(com.apple.access_ssh) pwd | tee -a $LF pwd tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log /Applications/freesurfer/subjects/fMRI uname -a | tee -a $LF uname -a tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log Darwin iMac-di-Stefano.local 16.5.0 Darwin Kernel Version 16.5.0: Fri Mar 3 16:52:33 PST 2017; root:xnu-3789.51.2~3/RELEASE_X86_64 x86_64 date | tee -a $LF date tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log Tue May 16 17:51:18 CEST 2017 set StartTime = `date` ; set StartTime = `date` date if ( $SaveRes || $SaveResUnwhitened ) set MatlabSaveRes = 1 ; if ( 0 || 0 ) set MatlabSaveRes = 1 set funcstemspec = `getana -a $analysis -t funcstem-specified` set funcstemspec = `getana -a $analysis -t funcstem-specified` getana -a fc.lamgseed.surf.lh -t funcstem-specified if ( $funcstemspec ) set DoPreProc = 0 ; if ( 0 ) set DoPreProc = 0 if ( $DoPreProc ) then if ( 1 ) then foreach sess ( $SessList ) foreach sess ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP ) set sessbase = `basename $sess` ; set sessbase = `basename $sess` basename /Applications/freesurfer/subjects/fMRI/subj067_GROUP set sessdir = `dirname $sess` ; set sessdir = `dirname $sess` dirname /Applications/freesurfer/subjects/fMRI/subj067_GROUP set cmd = ( preproc-sess -s $sessbase -d $sessdir -a $analysis -nolog ) ; set cmd = ( preproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nolog ) echo $cmd | tee -a $LF tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log echo preproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nolog preproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nolog $cmd | tee -a $LF preproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nolog tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Stefano setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova Darwin iMac-di-Stefano.local 16.5.0 Darwin Kernel Version 16.5.0: Fri Mar 3 16:52:33 PST 2017; root:xnu-3789.51.2~3/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/fMRI /Applications/freesurfer/fsfast/bin/preproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nolog Tue May 16 17:51:20 CEST 2017 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain subj067_GROUP Template ----------------------------- mktemplate-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -fsd rest -nolog -update Session: /Applications/freesurfer/subjects/fMRI/subj067_GROUP ---------------- Tue May 16 17:51:20 CEST 2017 Detected input format at nii subj067_GROUP Update not needed Run: 001 ---------------- Tue May 16 17:51:20 CEST 2017 subj067_GROUP 001 Update not needed Tue May 16 17:51:20 CEST 2017 mktemplate-sess completed subj067_GROUP Registration ----------------------------- register-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -fsd rest -delete-dat -dof 6 -bold -per-run -nolog -update -init-coreg -------------------------------------------------------------- register-sess logfile is /dev/null -------------------------------------------------------------- Tue May 16 17:51:21 CEST 2017 setenv SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova cd /Applications/freesurfer/subjects/fMRI /Applications/freesurfer/fsfast/bin/register-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -fsd rest -delete-dat -dof 6 -bold -per-run -nolog -update -init-coreg freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Darwin iMac-di-Stefano.local 16.5.0 Darwin Kernel Version 16.5.0: Fri Mar 3 16:52:33 PST 2017; root:xnu-3789.51.2~3/RELEASE_X86_64 x86_64 Session: /Applications/freesurfer/subjects/fMRI/subj067_GROUP ---------------- Tue May 16 17:51:21 CEST 2017 /Applications/freesurfer/subjects/fMRI/subj067_GROUP Run: 001 ---------------- Tue May 16 17:51:21 CEST 2017 Update not needed Tue May 16 17:51:21 CEST 2017 register-sess completed subj067_GROUP Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd rest -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -per-run -nolog -update ------------------------------------------------ /Applications/freesurfer/subjects/fMRI/subj067_GROUP Tue May 16 17:51:21 CEST 2017 subj067_GROUP Update not needed for session-level mask subj067_GROUP Update not needed for run 001 mask meanval --i stem2fname stem Looks for stem.fmt where fmt is mgh mgz nii nii.gz bhdr img w, then returns stem.fmt. See also stem2fmt, fname2stem The file needs to exist on disk. --m 001/masks/brain.e3.nii.gz --o 001/global.meanval.dat --avgwf 001/global.waveform.dat ERROR: cannot find stem2fname if ( $status ) exit 1 ; if ( 1 ) exit 1 exit 1 Thanks ----Messaggio originale---- Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> Data: 16-mag-2017 17.21 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] selxavg3-sess error not sure what is going on. Is the script stem2fname in your path? If so, run selxavg3-sess with -debug as the first option and send the terminal output On 5/16/17 3:08 AM, stdp82(a)virgilio.it wrote: Hi list, this error occurs during selxavg3-sess in FS-FAST fcMRI meanval --i stem2fname stem Looks for stem.fmt where fmt is mgh mgz nii nii.gz bhdr img w, then returns stem.fmt. See also stem2fmt, fname2stem The file needs to exist on disk. --m 001/masks/brain.e3.nii.gz --o 001/global.meanval.dat --avgwf 001/global.waveform.dat ERROR: cannot find stem2fname I have already run for this folder other seed. The error occurs only on it (amygdala). Thanks Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

(no subject)
by Gamaliz 16 May '17

16 May '17

Bruce, I tried mris_fill, but it gives me a filled white matter volume (I already have that in the mri directory. I need the contour only. Douglas, Looking into the --help gave me a few ideas. I think the help page (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol ) should include this information. I was able to create the volume by adding --identity, --template, and --mkmask. The required surfval and volreg, are taken from the -mkmask and identity respectively. The surface is created using the template from T1.mgz,, -mkmask works for me. However the orientation is wrong (and thus the registration). I wonder which file contains the correct registration (to give it as input to volreg. I tried using fstal 1 (this sets the template to mni305.cor.subfov1res.mgz and registration from mni305.cor.subfov1res.reg: That also gave me an unregistered output. [image: Inline image 2] [image: Inline image 1] I guess the only piece of the puzzle I am missing is which registration file to use, so that the final volume is registered to the T1.mgz. This file must be there, as when loading the images into tkmedit they are registered. here is the output of the execution. The reg files comes from using --identity. I wonder which reg file can I use. test@ubuntudev12:~/Desktop/surftovol/user_id$ mri_surf2vol --mkmask --surf white --hemi lh --o out.nii.gz --template mri/T1.mgz --sd /home/test/Desktop/surftovol/ --subject user_id --identity user_id gdiagno = -1 Using identity matrix for registration Overriding reg subject user_id with user_id Qa2v: SurfXYZ to VolCRS: ------------------------------ -1.000 0.000 0.000 128.000; 0.000 0.000 -1.000 128.000; 0.000 1.000 0.000 128.000; 0.000 0.000 0.000 1.000; -------------------------------------------------- subjects dir /home/test/Desktop/surftovol/ hemi lh mksurfmask 1 projfrac 0 outvol path out.nii.gz template path mri/T1.mgz ------- Anat2Vol Registration (TkReg)---- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ----------------------------------------- height = 256 width = 256 depth = 256 xsize = 1.000000 ysize = 1.000000 zsize = 1.000000 cdc = -1.000000 0.000000 0.000000 rdc = 0.000000 0.000000 -1.000000 sdc = 0.000000 1.000000 -0.000000 xyz0 = -8.411377 8.796127 -0.092697 Gdiag_no -1 Reading surface /home/test/Desktop/surftovol//user_id/surf/lh.white Done reading source surface surf nframes = 1 INFO: mapping vertices to closest voxel INFO: resampling surface to volume INFO: sampled 61045 voxels in the volume INFO: writing output volume to out.nii.gz done test@ubuntudev12:~/Desktop/surftovol/user_id$ mri_surf2vol --mkmask --surf white --hemi lh --o out.nii.gz --template mri/T1.mgz --sd /home/test/Desktop/surftovol/ --subject user_id --identity user_id On Tue, May 16, 2017 at 11:08 AM, Douglas Greve <greve(a)nmr.mgh.harvard.edu> wrote: > If you run it with --help, it will print out examples. Did you try that? > > On 5/16/17 9:26 AM, Bruce Fischl wrote: > > Hi gAbE > > you could try using mris_fill, or even mris_compute_volume_fractions > > cheers > Bruce > On Mon, 15 May 2017, Gamaliz wrote: > > > My idea is to convert the registered white surface into a volume, so it > can be shown in a volume viewer (not a surface viewer). I need to display a > DTI image and mark the edges of the white matter as a line on top if it. > This is not the exact command, I am not sitting in front of my station, > but it goes something like it. I tried many combinations, the general error > was related to the template files not on the correct format (it could have > been they couldn't be found to be opened too, the error seemed generic). > mri_surf2vol --surfval white --hemi lh --outvol test.mgz --template > T1.mgz > --volreg T1.mgz --sd /home/user/Desktop/sf/sub1 > I am at a loss for the --volreg flag. > The sd seems to indicate the directory of freesurfer (but then how is the > co > mmand aware of the specficic subject I am trying to process? I tried > using: --identity subject no luck. > 'sub1' us my subject, located not in the default freesurfer directory. > There are no examples or a lot of help using it > https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol > > If this is not enough I can get back to you with the specific error > tomorrow > . > On Mon, May 15, 2017 at 10:02 PM, Douglas Greve > > <greve(a)nmr.mgh.harvard.edu> <greve(a)nmr.mgh.harvard.edu> > > wrote: > > what was your mri_surf2vol cmd line? And what was the terminal > output? > > > On 5/15/17 9:59 PM, Gamaliz wrote: > I looked at the ribbon.mgz, but it is a pial surface, not > really delineated white matter the way I need it. There is > a command called mri_sur2vol, I have tried to use it, but > unsuccessfully, no idea if that is the solution to my > problem. > > On Mon, May 15, 2017 at 9:57 PM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu> <greve(a)nmr.mgh.harvard.edu> wrote: > > not sure what you mean. Have you looked at the > ribbon.mgz file? > > > On 5/15/17 5:20 PM, Gamaliz wrote: > I need to create an image which overlaps the > T1/mgz and the outer surface of the white > matter. How do I convert the surface into a > mgz volume? > > > -- > gAbE > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer > mailing list Freesurfer(a)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. > > -- gAbE > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. > > > > > -- > gAbE > > > > > _______________________________________________ > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. > > -- gAbE

2 1

R: Re: R: Re: selxavg3-sess error
by stdp82＠virgilio.it 16 May '17

16 May '17

Yes, the file exists.Additionally, please take in account that I have run other FC analysis on this subj using other seed as ROI. ----Messaggio originale---- Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> Data: 16-mag-2017 18.21 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: selxavg3-sess error Does this file exist ? /Applications/freesurfer/subjects/fMRI/subj067_GROUP/001/masks/brain.e3.nii.gz You can try deleting the /Applications/freesurfer/subjects/fMRI/subj067_GROUP/001/masks folder and re-running. On 5/16/17 11:53 AM, stdp82(a)virgilio.it wrote: selxavg3-sess -s subj067_GROUP -a fc.lamgseed.surf.lh -debug set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return foreach grp ( $grpdefs ) foreach grp ( ) goto check_params ; goto check_params if ( $#SessList == 0 ) then if ( 1 == 0 ) then if ( $#SearchPathList == 0 ) then if ( 0 == 0 ) then set SearchPathList = "." ; set SearchPathList = . endif endif goto check_params_return ; goto check_params_return set UniqueList = ( ) ; set UniqueList = ( ) foreach d ( $SearchPathList ) foreach d ( . ) if ( ! -e $d ) then if ( ! -e . ) then set IsUnique = 1 ; set IsUnique = 1 foreach u ( $UniqueList ) foreach u ( ) if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ; if ( 1 ) set UniqueList = ( . ) set UniqueList = ( . ) end end set SearchPathList = ( $UniqueList ) ; set SearchPathList = ( . ) set errs = 0 ; set errs = 0 set SessPath = ( ) ; set SessPath = ( ) foreach sess ( $SessList ) foreach sess ( subj067_GROUP ) set tmp = ( ) ; set tmp = ( ) foreach d ( $SearchPathList ) foreach d ( . ) set stst = $d/$sess set stst = ./subj067_GROUP if ( -d $stst ) then if ( -d ./subj067_GROUP ) then if ( ! -r $stst ) then if ( ! -r ./subj067_GROUP ) then pushd $stst > /dev/null ; pushd ./subj067_GROUP set tmp = ( $tmp `$PWDCMD` ) ; set tmp = ( `$PWDCMD` ) pwd popd > /dev/null ; popd endif endif end end set nfound = ( $#tmp ) ; set nfound = ( 1 ) if ( $nfound == 0 ) then if ( 1 == 0 ) then if ( $nfound > 1 ) then if ( 1 > 1 ) then set SessPath = ( $SessPath $tmp ) ; set SessPath = ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP ) end end set UniqueList = ( ) ; set UniqueList = ( ) foreach s ( $SessPath ) foreach s ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP ) set IsUnique = 1 ; set IsUnique = 1 foreach u ( $UniqueList ) foreach u ( ) if ( ! $IsUnique && ! $AllowRedundant ) then if ( ! 1 && ! 0 ) then set UniqueList = ( $UniqueList $s ) ; set UniqueList = ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP ) endif endif end end echo $SessPath echo /Applications/freesurfer/subjects/fMRI/subj067_GROUP exit $errs ; exit 0 set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params if ( $#SessList == 0 ) then if ( 1 == 0 ) then if ( $#analysis == 0 && $flacfile == 0 ) then if ( 1 == 0 && == 0 ) then if ( $#analysis != 0 ) then if ( 1 != 0 ) then if ( ! -d $analysis ) then if ( ! -d fc.lamgseed.surf.lh ) then if ( ! -e $analysis/analysis.info ) then if ( ! -e fc.lamgseed.surf.lh/analysis.info ) then endif endif if ( $#flacfile != 0 ) then if ( 0 != 0 ) then if ( $perrun && $jkrun ) then if ( 0 && 0 ) then if ( $UseOctave ) then if ( 0 ) then if ( $#DoneFile ) then if ( 0 ) then goto check_params_return ; goto check_params_return set StudyDir = `pwd` ; set StudyDir = `pwd` pwd if ( $#analysis ) then if ( 1 ) then set analysisname = $analysis set analysisname = fc.lamgseed.surf.lh set fsd = `getana -a $analysis -t fsd` ; set fsd = `getana -a $analysis -t fsd` getana -a fc.lamgseed.surf.lh -t fsd set PerSession = `getana -a $analysis -t IsPerSession` set PerSession = `getana -a $analysis -t IsPerSession` getana -a fc.lamgseed.surf.lh -t IsPerSession set IsNative = `getana -a $analysis -t IsNative` set IsNative = `getana -a $analysis -t IsNative` getana -a fc.lamgseed.surf.lh -t IsNative set IsSurface = `getana -a $analysis -t IsSurface` set IsSurface = `getana -a $analysis -t IsSurface` getana -a fc.lamgseed.surf.lh -t IsSurface if ( $IsSurface ) then if ( 1 ) then set subject = `getana -a $analysis -t subject` set subject = `getana -a $analysis -t subject` getana -a fc.lamgseed.surf.lh -t subject set hemi = `getana -a $analysis -t hemi` set hemi = `getana -a $analysis -t hemi` getana -a fc.lamgseed.surf.lh -t hemi echo "Surface data $subject $hemi" echo Surface data fsaverage lh Surface data fsaverage lh endif endif set dt = `getana -a $analysis -t designtype` set dt = `getana -a $analysis -t designtype` getana -a fc.lamgseed.surf.lh -t designtype if ( $dt == "abblocked" ) set RequireContrasts = 0 ; if ( notask == abblocked ) set RequireContrasts = 0 if ( $dt == "retinotopy" ) set RequireContrasts = 0 ; if ( notask == retinotopy ) set RequireContrasts = 0 set contrasts = `getana -a $analysis -t contrasts` set contrasts = `getana -a $analysis -t contrasts` getana -a fc.lamgseed.surf.lh -t contrasts if ( $#contrasts == 0 && $RequireContrasts ) then if ( 1 == 0 && 1 ) then endif endif if ( $#LF == 0 ) then if ( 0 == 0 ) then if ( $nolog ) then if ( 0 ) then if ( $#OutParent == 0 ) then if ( 0 == 0 ) then set logdir = `pwd`/log ; set logdir = `pwd`/log pwd else else mkdir -p $logdir mkdir -p /Applications/freesurfer/subjects/fMRI/log if ( ! -e $logdir ) then if ( ! -e /Applications/freesurfer/subjects/fMRI/log ) then set LF = $logdir/selxavg3-sess-$fsd-$analysis-$DateStr.log set LF = /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log if ( -e $LF ) mv $LF $LF.old if ( -e /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log ) mv /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log.old endif endif endif endif endif endif echo "--------------------------------------------------------------" echo -------------------------------------------------------------- -------------------------------------------------------------- echo "selxavg3-sess logfile is $LF" echo selxavg3-sess logfile is /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log selxavg3-sess logfile is /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log echo "--------------------------------------------------------------" echo -------------------------------------------------------------- -------------------------------------------------------------- echo "selxavg3-sess log file" | tee -a $LF tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log echo selxavg3-sess log file selxavg3-sess log file echo $0 | tee -a $LF tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log echo /Applications/freesurfer/fsfast/bin/selxavg3-sess /Applications/freesurfer/fsfast/bin/selxavg3-sess echo $inputargs | tee -a $LF tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log echo -s subj067_GROUP -a fc.lamgseed.surf.lh -debug -s subj067_GROUP -a fc.lamgseed.surf.lh -debug echo $VERSION | tee -a $LF tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log echo $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ id | tee -a $LF id tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log uid=501(Stefano) gid=20(staff) groups=20(staff),402(com.apple.sharepoint.group.1),12(everyone),61(localaccounts),79(_appserverusr),80(admin),81(_appserveradm),98(_lpadmin),33(_appstore),100(_lpoperator),204(_developer),395(com.apple.access_ftp),398(com.apple.access_screensharing),399(com.apple.access_ssh) pwd | tee -a $LF pwd tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log /Applications/freesurfer/subjects/fMRI uname -a | tee -a $LF uname -a tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log Darwin iMac-di-Stefano.local 16.5.0 Darwin Kernel Version 16.5.0: Fri Mar 3 16:52:33 PST 2017; root:xnu-3789.51.2~3/RELEASE_X86_64 x86_64 date | tee -a $LF date tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log Tue May 16 17:51:18 CEST 2017 set StartTime = `date` ; set StartTime = `date` date if ( $SaveRes || $SaveResUnwhitened ) set MatlabSaveRes = 1 ; if ( 0 || 0 ) set MatlabSaveRes = 1 set funcstemspec = `getana -a $analysis -t funcstem-specified` set funcstemspec = `getana -a $analysis -t funcstem-specified` getana -a fc.lamgseed.surf.lh -t funcstem-specified if ( $funcstemspec ) set DoPreProc = 0 ; if ( 0 ) set DoPreProc = 0 if ( $DoPreProc ) then if ( 1 ) then foreach sess ( $SessList ) foreach sess ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP ) set sessbase = `basename $sess` ; set sessbase = `basename $sess` basename /Applications/freesurfer/subjects/fMRI/subj067_GROUP set sessdir = `dirname $sess` ; set sessdir = `dirname $sess` dirname /Applications/freesurfer/subjects/fMRI/subj067_GROUP set cmd = ( preproc-sess -s $sessbase -d $sessdir -a $analysis -nolog ) ; set cmd = ( preproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nolog ) echo $cmd | tee -a $LF tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log echo preproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nolog preproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nolog $cmd | tee -a $LF preproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nolog tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Stefano setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova Darwin iMac-di-Stefano.local 16.5.0 Darwin Kernel Version 16.5.0: Fri Mar 3 16:52:33 PST 2017; root:xnu-3789.51.2~3/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/fMRI /Applications/freesurfer/fsfast/bin/preproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nolog Tue May 16 17:51:20 CEST 2017 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain subj067_GROUP Template ----------------------------- mktemplate-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -fsd rest -nolog -update Session: /Applications/freesurfer/subjects/fMRI/subj067_GROUP ---------------- Tue May 16 17:51:20 CEST 2017 Detected input format at nii subj067_GROUP Update not needed Run: 001 ---------------- Tue May 16 17:51:20 CEST 2017 subj067_GROUP 001 Update not needed Tue May 16 17:51:20 CEST 2017 mktemplate-sess completed subj067_GROUP Registration ----------------------------- register-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -fsd rest -delete-dat -dof 6 -bold -per-run -nolog -update -init-coreg -------------------------------------------------------------- register-sess logfile is /dev/null -------------------------------------------------------------- Tue May 16 17:51:21 CEST 2017 setenv SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova cd /Applications/freesurfer/subjects/fMRI /Applications/freesurfer/fsfast/bin/register-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -fsd rest -delete-dat -dof 6 -bold -per-run -nolog -update -init-coreg freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Darwin iMac-di-Stefano.local 16.5.0 Darwin Kernel Version 16.5.0: Fri Mar 3 16:52:33 PST 2017; root:xnu-3789.51.2~3/RELEASE_X86_64 x86_64 Session: /Applications/freesurfer/subjects/fMRI/subj067_GROUP ---------------- Tue May 16 17:51:21 CEST 2017 /Applications/freesurfer/subjects/fMRI/subj067_GROUP Run: 001 ---------------- Tue May 16 17:51:21 CEST 2017 Update not needed Tue May 16 17:51:21 CEST 2017 register-sess completed subj067_GROUP Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd rest -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -per-run -nolog -update ------------------------------------------------ /Applications/freesurfer/subjects/fMRI/subj067_GROUP Tue May 16 17:51:21 CEST 2017 subj067_GROUP Update not needed for session-level mask subj067_GROUP Update not needed for run 001 mask meanval --i stem2fname stem Looks for stem.fmt where fmt is mgh mgz nii nii.gz bhdr img w, then returns stem.fmt. See also stem2fmt, fname2stem The file needs to exist on disk. --m 001/masks/brain.e3.nii.gz --o 001/global.meanval.dat --avgwf 001/global.waveform.dat ERROR: cannot find stem2fname if ( $status ) exit 1 ; if ( 1 ) exit 1 exit 1 Thanks ----Messaggio originale---- Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> Data: 16-mag-2017 17.21 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] selxavg3-sess error not sure what is going on. Is the script stem2fname in your path? If so, run selxavg3-sess with -debug as the first option and send the terminal output On 5/16/17 3:08 AM, stdp82(a)virgilio.it wrote: Hi list, this error occurs during selxavg3-sess in FS-FAST fcMRI meanval --i stem2fname stem Looks for stem.fmt where fmt is mgh mgz nii nii.gz bhdr img w, then returns stem.fmt. See also stem2fmt, fname2stem The file needs to exist on disk. --m 001/masks/brain.e3.nii.gz --o 001/global.meanval.dat --avgwf 001/global.waveform.dat ERROR: cannot find stem2fname I have already run for this folder other seed. The error occurs only on it (amygdala). Thanks Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

R: Re: selxavg3-sess error
by stdp82＠virgilio.it 16 May '17

16 May '17

selxavg3-sess -s subj067_GROUP -a fc.lamgseed.surf.lh -debugset echo = 1 ;breakswbreaksw endendwhile ( $#argv != 0 )while ( 0 != 0 )goto parse_args_return ;goto parse_args_return foreach grp ( $grpdefs )foreach grp ( ) goto check_params ;goto check_params if ( $#SessList == 0 ) thenif ( 1 == 0 ) then if ( $#SearchPathList == 0 ) thenif ( 0 == 0 ) thenset SearchPathList = "." ;set SearchPathList = .endifendif goto check_params_return ;goto check_params_return set UniqueList = ( ) ;set UniqueList = ( )foreach d ( $SearchPathList )foreach d ( . )if ( ! -e $d ) thenif ( ! -e . ) then set IsUnique = 1 ;set IsUnique = 1foreach u ( $UniqueList )foreach u ( )if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ;if ( 1 ) set UniqueList = ( . )set UniqueList = ( . )endend set SearchPathList = ( $UniqueList ) ;set SearchPathList = ( . ) set errs = 0 ;set errs = 0 set SessPath = ( ) ;set SessPath = ( )foreach sess ( $SessList )foreach sess ( subj067_GROUP )set tmp = ( ) ;set tmp = ( )foreach d ( $SearchPathList )foreach d ( . )set stst = $d/$sessset stst = ./subj067_GROUPif ( -d $stst ) thenif ( -d ./subj067_GROUP ) thenif ( ! -r $stst ) thenif ( ! -r ./subj067_GROUP ) thenpushd $stst > /dev/null ;pushd ./subj067_GROUPset tmp = ( $tmp `$PWDCMD` ) ;set tmp = ( `$PWDCMD` )pwdpopd > /dev/null ;popdendifendifendendset nfound = ( $#tmp ) ;set nfound = ( 1 )if ( $nfound == 0 ) thenif ( 1 == 0 ) thenif ( $nfound > 1 ) thenif ( 1 > 1 ) thenset SessPath = ( $SessPath $tmp ) ;set SessPath = ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP )endend set UniqueList = ( ) ;set UniqueList = ( )foreach s ( $SessPath )foreach s ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP )set IsUnique = 1 ;set IsUnique = 1foreach u ( $UniqueList )foreach u ( )if ( ! $IsUnique && ! $AllowRedundant ) thenif ( ! 1 && ! 0 ) then set UniqueList = ( $UniqueList $s ) ;set UniqueList = ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP )endifendifendend echo $SessPathecho /Applications/freesurfer/subjects/fMRI/subj067_GROUP exit $errs ;exit 0set echo = 1 ;breakswbreaksw endendwhile ( $#argv != 0 )while ( 0 != 0 ) goto parse_args_return ;goto parse_args_return goto check_params ;goto check_params if ( $#SessList == 0 ) thenif ( 1 == 0 ) thenif ( $#analysis == 0 && $flacfile == 0 ) thenif ( 1 == 0 && == 0 ) thenif ( $#analysis != 0 ) thenif ( 1 != 0 ) thenif ( ! -d $analysis ) thenif ( ! -d fc.lamgseed.surf.lh ) thenif ( ! -e $analysis/analysis.info ) thenif ( ! -e fc.lamgseed.surf.lh/analysis.info ) thenendifendifif ( $#flacfile != 0 ) thenif ( 0 != 0 ) thenif ( $perrun && $jkrun ) thenif ( 0 && 0 ) then if ( $UseOctave ) thenif ( 0 ) then if ( $#DoneFile ) thenif ( 0 ) then goto check_params_return ;goto check_params_return set StudyDir = `pwd` ;set StudyDir = `pwd`pwd if ( $#analysis ) thenif ( 1 ) then set analysisname = $analysisset analysisname = fc.lamgseed.surf.lhset fsd = `getana -a $analysis -t fsd` ;set fsd = `getana -a $analysis -t fsd`getana -a fc.lamgseed.surf.lh -t fsdset PerSession = `getana -a $analysis -t IsPerSession`set PerSession = `getana -a $analysis -t IsPerSession`getana -a fc.lamgseed.surf.lh -t IsPerSessionset IsNative = `getana -a $analysis -t IsNative`set IsNative = `getana -a $analysis -t IsNative`getana -a fc.lamgseed.surf.lh -t IsNativeset IsSurface = `getana -a $analysis -t IsSurface`set IsSurface = `getana -a $analysis -t IsSurface`getana -a fc.lamgseed.surf.lh -t IsSurfaceif ( $IsSurface ) thenif ( 1 ) thenset subject = `getana -a $analysis -t subject`set subject = `getana -a $analysis -t subject`getana -a fc.lamgseed.surf.lh -t subjectset hemi = `getana -a $analysis -t hemi`set hemi = `getana -a $analysis -t hemi`getana -a fc.lamgseed.surf.lh -t hemiecho "Surface data $subject $hemi"echo Surface data fsaverage lhSurface data fsaverage lhendifendifset dt = `getana -a $analysis -t designtype`set dt = `getana -a $analysis -t designtype`getana -a fc.lamgseed.surf.lh -t designtypeif ( $dt == "abblocked" ) set RequireContrasts = 0 ;if ( notask == abblocked ) set RequireContrasts = 0if ( $dt == "retinotopy" ) set RequireContrasts = 0 ;if ( notask == retinotopy ) set RequireContrasts = 0set contrasts = `getana -a $analysis -t contrasts`set contrasts = `getana -a $analysis -t contrasts`getana -a fc.lamgseed.surf.lh -t contrastsif ( $#contrasts == 0 && $RequireContrasts ) thenif ( 1 == 0 && 1 ) thenendifendif if ( $#LF == 0 ) thenif ( 0 == 0 ) thenif ( $nolog ) thenif ( 0 ) then if ( $#OutParent == 0 ) thenif ( 0 == 0 ) thenset logdir = `pwd`/log ;set logdir = `pwd`/logpwdelseelsemkdir -p $logdirmkdir -p /Applications/freesurfer/subjects/fMRI/logif ( ! -e $logdir ) thenif ( ! -e /Applications/freesurfer/subjects/fMRI/log ) then set LF = $logdir/selxavg3-sess-$fsd-$analysis-$DateStr.logset LF = /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logif ( -e $LF ) mv $LF $LF.oldif ( -e /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log ) mv /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log.oldendifendifendifendifendifendifecho "--------------------------------------------------------------"echo ----------------------------------------------------------------------------------------------------------------------------echo "selxavg3-sess logfile is $LF"echo selxavg3-sess logfile is /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logselxavg3-sess logfile is /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logecho "--------------------------------------------------------------"echo ---------------------------------------------------------------------------------------------------------------------------- echo "selxavg3-sess log file" | tee -a $LFtee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logecho selxavg3-sess log fileselxavg3-sess log fileecho $0 | tee -a $LFtee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logecho /Applications/freesurfer/fsfast/bin/selxavg3-sess/Applications/freesurfer/fsfast/bin/selxavg3-sessecho $inputargs | tee -a $LFtee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logecho -s subj067_GROUP -a fc.lamgseed.surf.lh -debug-s subj067_GROUP -a fc.lamgseed.surf.lh -debugecho $VERSION | tee -a $LFtee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logecho $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $id | tee -a $LFidtee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.loguid=501(Stefano) gid=20(staff) groups=20(staff),402(com.apple.sharepoint.group.1),12(everyone),61(localaccounts),79(_appserverusr),80(admin),81(_appserveradm),98(_lpadmin),33(_appstore),100(_lpoperator),204(_developer),395(com.apple.access_ftp),398(com.apple.access_screensharing),399(com.apple.access_ssh)pwd | tee -a $LFpwdtee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log/Applications/freesurfer/subjects/fMRIuname -a | tee -a $LFuname -atee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logDarwin iMac-di-Stefano.local 16.5.0 Darwin Kernel Version 16.5.0: Fri Mar 3 16:52:33 PST 2017; root:xnu-3789.51.2~3/RELEASE_X86_64 x86_64date | tee -a $LFdatetee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logTue May 16 17:51:18 CEST 2017 set StartTime = `date` ;set StartTime = `date`date if ( $SaveRes || $SaveResUnwhitened ) set MatlabSaveRes = 1 ;if ( 0 || 0 ) set MatlabSaveRes = 1 set funcstemspec = `getana -a $analysis -t funcstem-specified`set funcstemspec = `getana -a $analysis -t funcstem-specified`getana -a fc.lamgseed.surf.lh -t funcstem-specifiedif ( $funcstemspec ) set DoPreProc = 0 ;if ( 0 ) set DoPreProc = 0 if ( $DoPreProc ) thenif ( 1 ) thenforeach sess ( $SessList )foreach sess ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP )set sessbase = `basename $sess` ;set sessbase = `basename $sess`basename /Applications/freesurfer/subjects/fMRI/subj067_GROUPset sessdir = `dirname $sess` ;set sessdir = `dirname $sess`dirname /Applications/freesurfer/subjects/fMRI/subj067_GROUPset cmd = ( preproc-sess -s $sessbase -d $sessdir -a $analysis -nolog ) ;set cmd = ( preproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nolog ) echo $cmd | tee -a $LFtee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logecho preproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nologpreproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nolog$cmd | tee -a $LFpreproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nologtee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log--------------------------------------------------------------preproc-sess logfile is /dev/null--------------------------------------------------------------$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $Stefanosetenv FREESURFER_HOME /Applications/freesurfersetenv SUBJECTS_DIR /Applications/freesurfer/subjects/subject_provaDarwin iMac-di-Stefano.local 16.5.0 Darwin Kernel Version 16.5.0: Fri Mar 3 16:52:33 PST 2017; root:xnu-3789.51.2~3/RELEASE_X86_64 x86_64/Applications/freesurfer/subjects/fMRI/Applications/freesurfer/fsfast/bin/preproc-sess-s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nologTue May 16 17:51:20 CEST 2017instem f mc 1 f fmcpr stc 0 fmcprsm 0 mask 1 brainsubj067_GROUP Template -----------------------------mktemplate-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -fsd rest -nolog -update Session: /Applications/freesurfer/subjects/fMRI/subj067_GROUP ----------------Tue May 16 17:51:20 CEST 2017Detected input format at niisubj067_GROUP Update not needed Run: 001 ---------------- Tue May 16 17:51:20 CEST 2017 subj067_GROUP 001 Update not neededTue May 16 17:51:20 CEST 2017mktemplate-sess completed subj067_GROUP Registration -----------------------------register-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -fsd rest -delete-dat -dof 6 -bold -per-run -nolog -update -init-coreg--------------------------------------------------------------register-sess logfile is /dev/null--------------------------------------------------------------Tue May 16 17:51:21 CEST 2017 setenv SUBJECTS_DIR /Applications/freesurfer/subjects/subject_provacd /Applications/freesurfer/subjects/fMRI/Applications/freesurfer/fsfast/bin/register-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -fsd rest -delete-dat -dof 6 -bold -per-run -nolog -update -init-coreg freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96cDarwin iMac-di-Stefano.local 16.5.0 Darwin Kernel Version 16.5.0: Fri Mar 3 16:52:33 PST 2017; root:xnu-3789.51.2~3/RELEASE_X86_64 x86_64 Session: /Applications/freesurfer/subjects/fMRI/subj067_GROUP ----------------Tue May 16 17:51:21 CEST 2017/Applications/freesurfer/subjects/fMRI/subj067_GROUP Run: 001 ----------------Tue May 16 17:51:21 CEST 2017Update not neededTue May 16 17:51:21 CEST 2017register-sess completed subj067_GROUP Mask ------------------------mkbrainmask-sess -maskstem brain -fsd rest -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -per-run -nolog -update------------------------------------------------/Applications/freesurfer/subjects/fMRI/subj067_GROUP Tue May 16 17:51:21 CEST 2017subj067_GROUP Update not needed for session-level masksubj067_GROUP Update not needed for run 001 maskmeanval --i stem2fname stem Looks for stem.fmt where fmt is mgh mgz nii nii.gz bhdr img w, then returns stem.fmt. See also stem2fmt, fname2stem The file needs to exist on disk. --m 001/masks/brain.e3.nii.gz --o 001/global.meanval.dat --avgwf 001/global.waveform.datERROR: cannot find stem2fnameif ( $status ) exit 1 ;if ( 1 ) exit 1exit 1 Thanks ----Messaggio originale---- Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> Data: 16-mag-2017 17.21 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] selxavg3-sess error not sure what is going on. Is the script stem2fname in your path? If so, run selxavg3-sess with -debug as the first option and send the terminal output On 5/16/17 3:08 AM, stdp82(a)virgilio.it wrote: Hi list, this error occurs during selxavg3-sess in FS-FAST fcMRI meanval --i stem2fname stem Looks for stem.fmt where fmt is mgh mgz nii nii.gz bhdr img w, then returns stem.fmt. See also stem2fmt, fname2stem The file needs to exist on disk. --m 001/masks/brain.e3.nii.gz --o 001/global.meanval.dat --avgwf 001/global.waveform.dat ERROR: cannot find stem2fname I have already run for this folder other seed. The error occurs only on it (amygdala). Thanks Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Volume comparison between groups and QDEC
by John Anderson 16 May '17

16 May '17

Hi Doug, Why Qdec offer "volume, area, thickness ,...etc " in the drop down menu "measures"? In this menu there are many measures and I understand that I can run surface based analysis depending on the choice of this drop down menu. Is this Correct? Please see attached. Thank you for any clarification I'm not sure I follow. If I understand, you are finding sig diff in PCG volume when you extract it the volume value for each subject (scaled by etiv) and process in SPSS. The part I don't understand is what you are doing with QDEC. I don't think QDEC can be used to test ROI volume. On 05/09/2017 05:58 PM, John Anderson wrote: > Dear Dr Doug, > I have two groups of subjects (80 patients and 40 controls). I > analyzed the data using Freesurfer v6.0. > I want to study the difference between the groups in "precentral gyrus > volume". After "recon-all" I built Qdec table and I used Qdec to > compute the comparison by including eTIV a covariate. After correcting > the results using Monte Carlo simulation or adjusting for FDR I found > no difference between the groups in volume neither in surface area. > > I adjusted the precentral gyrus volume values for eTIV using the commands: > > mri_label_volume -eTIV $SUBJECTS_DIR/${i}/mri/transforms/talairach.xfm > 1948 $SUBJECTS_DIR/${i}/mri/wmparc.mgz 2017 mri_label_volume -eTIV > $SUBJECTS_DIR/${i}/mri/transforms/talairach.xfm > 1948 $SUBJECTS_DIR/${i}/mri/wmparc.mgz 2024 > > I extracted the adjusted volume values to SPSS then I ran box plots > comparison between the groups and I found difference at (P<0.0001) Why > Qdec doesn't show the difference between the groups although the p > value is very small. What I am doing wrong in Qdec? Is it wrong to > include eTIV a covariate? > > Thank you for any advice > John > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ��1�E�

2 1

Volumen for Aparc+aseg region 2 and 41
by Gamaliz 16 May '17

16 May '17

Regions 2 and 41 are labeled as Left-Cerebral-White-Matter Right-Cerebral-White-Matter respectively. However, there is no label in the aseg.stats, wmparc.stats or xh.aparc.stats files. The only label that seems to match it is the: CorticalWhiteMatterVol in aseg.stats. Where is the white matter (regions 2 and 4) volumes saved? is this equivalent to the cortical white matter values?

2 1

Maps showing correlations between structural measures
by Martin Juneja 16 May '17

16 May '17

Hello FreeSurfer experts, I came across a paper: http://www.sciencedirect.com/science/article/pii/S0166432815001837 where correlation maps between volume and gyrification are reported. I am familiar with GLM in FreeSurfer i.e. correlating behavioral measures with volume and gyrification but I was wondering how to correlate structure measures with each other e.g. volume and gyrification. I would really appreciate any help. Thanks.

3 11

problem in extract subcortical volume as ROI
by Cong 16 May '17

16 May '17

Dear FSers I extracted left thalamus as ROI volume from aseg.mgz by this command: mri_binarize --i control001/mri/aseg.mgz --match 10 --o control001/roi/l_thal.nii I overlaid l_thal.nii to control001.nii in MRIcro software in a Macbook and it looks well. However, when I overlaid l_thal.nii to control001.nii in Windows MRIcro, it comes a Warning: this NIFTI image includes an rotation transformation. When I open these two files same time, the left thalamus mismatch obviously to original T1 image. I attached an image to show my problem. I try to register this ROI volume to diffusion B0 image, and the registered left thalamus appears in the same wrong position as shown in attached image. Could someone tell me what’s wrong and how to solve it. Regards Cong

2 1

selxavg3-sess error
by stdp82＠virgilio.it 16 May '17

16 May '17

Hi list, this error occurs during selxavg3-sess in FS-FAST fcMRI meanval --i stem2fname stem Looks for stem.fmt where fmt is mgh mgz nii nii.gz bhdr img w, then returns stem.fmt. See also stem2fmt, fname2stem The file needs to exist on disk. --m 001/masks/brain.e3.nii.gz --o 001/global.meanval.dat --avgwf 001/global.waveform.datERROR: cannot find stem2fname I have already run for this folder other seed. The error occurs only on it (amygdala). Thanks Stefano

2 1

perirhinal volumes
by Antoniades, Mathilde 16 May '17

16 May '17

Dear Freesurfer experts, I would like to obtain perirhinal cortex volumes from structural images that have undergone recon-all. I see that the label subfolder contains left and right perirhinal cortex labels but the stats file does not. So a first step seems to be "converting" the label to a stats file!? Is there a command for this? Thank you, Mathilde. PhD student in Psychosis studies.

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Freesurfer May 2017