Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30064 discussions

GCS file format specification and conversion to GIFTI
by Oscar Esteban 14 Mar '24

14 Mar '24

External Email - Use Caution Dear all, I'm trying to understand the GCS file format as I failed to try an easy conversion with mris_convert. If mris_convert cannot convert GCS to GIFTI, is there any open description of how the format is implemented? Thanks very much Best, Oscar *___________________________* *Oscar Esteban, Ph.D.* Research and Teaching Ambizione FNS Fellow Dept. of Radiology, CHUV, University of Lausanne +41 77 957 00 77 +1 (650) 733 33 82

2 1

mri_label2vol fillribbon issue
by Schneider, Letitia Maria 14 Mar '24

14 Mar '24

External Email - Use Caution Hello, I am using Freesurfer version 7.3.2 on a mac. I am using the mri_label2vol function to project an anatomical label into volume space, but I realised the label comes out wrong when I use the --fill-ribbon flag: its orientation changes to RSP. The same label comes out right when I use the --fillthresh flag (oriented in RPI). Any idea why using --fillribbon changes the orientation? Thank you in advance. Best wishes, Letitia

2 1

recon-all hard error: mris_calc could not establish read access to rh.area
by Ariko, Taylor 13 Mar '24

13 Mar '24

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to run the recon-all pipeline on one subject using the following code: recon-all -all -i t1.nii -s p03_1 Although, I get the following error in the command line: mris_calc -o rh.area.mid rh.area add rh.area.pial error: No such file or directory error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file error: No such file or directory error: mris_calc: could not establish read access to 'rh.area'. Tue Aug 1 15:58:13 EDT 2023 ERROR: vertexvol mris_calc -o rh.area.mid rh.area add rh.area.pial Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64 recon-all -s p03_8 exited with ERRORS at Tue Aug 1 15:58:13 EDT 2023 To report a problem, see http://secure-web.cisco.com/1dFtz9tfZWpoyZVj7mXFMLhzADOYxytPQ-lAzdm9SS0VD1F… The recon-all.error file contains: ------------------------------ SUBJECT p03_8 DATE Tue Aug 1 15:58:13 EDT 2023 USER taylorariko HOST C02F10PVPN5W.local PROCESSOR x86_64 OS Darwin Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64 7.2.0 (freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b) /Applications/freesurfer/7.2.0/bin/recon-all PWD /Volumes/Beta/Carmen/t1/p03_8/p03_8/mri CMD vertexvol --s p03_8 --rh --th3 I have made sure that I have read, write, and execute access to the folder /path/to/subject/surf and the file rh.area. I can successfully run the command to make rh.area (mris_place_surface --area-map ../surf/rh.white ../surf/rh.area), but the error persists in using rh.area. I have disk space and can run other commands such as this fake one (mris_calc -o rh.area.Test rh.area.pial add rh.area.pial), but not if it contains rh.area. I have tried to rerun the command from root and get the same error message. I found 2 similar threads of the mail-archive, though I didn’t find any remedies: 1. https://secure-web.cisco.com/1s_8L81vMyC0-KdGicsKrUniSkh4Egg5_LxXz-_YnmsgL0… 2. https://secure-web.cisco.com/1MW6Y468pIeNLaB3ruN22mzrkJIjqalKQmsNncuNqyZW9S… Does anyone have any thoughts on how to trouble-shoot this? I have included my recon-all.log in the case it is of any use. 1. Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b 2. Platform: macOS Sonoma 14.3.1 3. uname -a: Darwin C02F10PVPN5W.local 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:28:58 PST 2023; root:xnu-10002.81.5~7/RELEASE_X86_64 x86_64 4. recon-all.log: see attached Thanks in advance! Taylor Ariko

3 10

Unsubscribe from the mailing list
by Tina Zahrie 13 Mar '24

13 Mar '24

External Email - Use Caution Hi, I would like to unsubscribe from the mailing list. Thanks

1 0

[WARNING: ATTACHMENT UNSCANNED]mri_ca_normalize in recon-all -base generate blank norm.mgz
by Keshuo Lin 13 Mar '24

13 Mar '24

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to use Freesurfer 7.4.1 recon-all-clinical and longitudinal process for stroke study. 38 subjects out of 85 subjects failed to complete the longitudinal process. The error is mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /g/data/ey6/keshuo/strokog/sss/freesurfer_result/threetime/000216RRW_template/mri/transforms/cc_up.lta 000216RRW_template error: mri_cc: no WM voxels found with norm > 40 -- check skull stripping I checked the previous steps between successful subjects and unsuccessful subjects. The norm.mgz generated from mri_ca_normalize are different. The subject_template/mri/norm.mgz of unsuccessful subjects are blank. The issue is because no control point was detected. Can you tell me how to solve this issue? I randomly attached one of the successful subjects and one of the unsuccessful subjects norm.mgz brainmask.mgz and norm_template.mgz. I have also attached the error recon-all log. Platform: I run the above codes in two OS systems: One is "Rocky Linux" VERSION="8.9 (Green Obsidian)" The other is Mac M2 chips with MACOS venture 13.3.1 Thanks for your time and patience. Best Regards, Keshuo Lin

1 0

Postdoctoral Position on PET and structural MRI/DTI at Brown University
by Topper, Mackenzie 12 Mar '24

12 Mar '24

External Email - Use Caution Position: Postdoctoral Position in Neuroimaging Research on Brain Aging and Alzheimer’s disease Area: Brain Aging and Alzheimer’s disease Department: Department of Psychiatry and Human Behavior Institution: Brown University We are seeking a highly motivated postdoctoral researcher to lead an NIH-funded project in the Laboratory for Cognitive and Translational Neuroscience (Director: Dr. Hwamee Oh) at Brown University. The project is to use amyloid and tau PET and structural MRI/DTI to study the impact of Alzheimer’s disease pathologies on structural and functional networks among cognitively normal older adults and patients with cognitive impairment. Applicants with a Ph.D. degree in cognitive neuroscience, computational neuroscience, biomedical engineering, or a relevant field are encouraged to apply. Prior experience with human neuroimaging in PET and/or structural MRI, and familiarity with programming in relevant languages (e.g., Python, MATLAB) are required. Applicants with experience with amyloid and tau PET or diffusion weighted imaging are especially encouraged to apply. The successful candidate is expected to demonstrate communication skills, motivation and interest in the area of neuroscience of cognitive and brain aging and Alzheimer’s disease, and the ability to independently develop research questions and work in collaboration with other team members. A preferred start date is Summer 2024, although it can be flexible. The position is primarily affiliated with the Department of Psychiatry and Human Behavior at Brown University. Interested applicants should email a brief description of research background and career goals, and CV with a list of 3 references to Dr. Hwamee Oh at hwamee_oh(a)brown.edu. Contact Website: https://secure-web.cisco.com/1NHAukz0oR4V4SHC4tbhOyQXDoh4Si5BlldXlY0aCBWiub… -- Mackenzie Topper Research Assistant & Lab Manager Oh Lab Brown University

1 0

Thalamic segmentation with FGATIR not running
by Amrita Pal 12 Mar '24

12 Mar '24

External Email - Use Caution Hi While doing thalamic segmentation with FGATIR additional volume, I am getting an error that "BIAS field corrected version of additional volume found; no need to recompute error: No such file or directory error: WARNING: 419053 NaNs found in volume tempT1.mgz.. and I get a blank ThalamicNucleiv.12.FGATIR.mgz Can you please help spot the error? Thanks and regards -- Amrita <http://secure-web.cisco.com/1_C1dP51_i2vV0jeUoIhLP19muStKl4Jj8_YmTeVMMckMui…> Virus-free.http://secure-web.cisco.com/1KBgLFDHeUPow5GUMM81SK3Q8c-uFtm-1aqc… <http://secure-web.cisco.com/1_C1dP51_i2vV0jeUoIhLP19muStKl4Jj8_YmTeVMMckMui…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

1 0

Postdoctoral position in human neuroscience at Boston University (Reinhart Lab)
by Wen Wen 11 Mar '24

11 Mar '24

External Email - Use Caution POSTDOCTORAL RESEARCHER POSITION AT BOSTON UNIVERSITY A position for a postdoctoral research associate in human cognitive neuroscience is available in the Reinhart Lab at Boston University, led by Associate Professor Rob Reinhart. The lab studies large-scale rhythmic neural mechanisms of perception and cognition in the human brain. Noninvasive brain stimulation techniques (HD-tACS, TI) are combined with electrophysiology (EEG) and source reconstruction (beamforming), neuroimaging (MRI, DTI, fMRI), and computational approaches (e.g., MVPA, RSA, DDM, RL, BHM). We are seeking an extremely motivated postdoctoral researcher with a background in human electrophysiology or neuroimaging. This is a unique opportunity in several respects. First, the postdoctoral associate will enjoy an extraordinary degree of intellectual freedom and creative control over their work, as our funding sources include large philanthropic gifts and fungible retention accounts, allowing us to pursue virtually any question that piques our curiosity. That said, our lab interests do tend to revolve around the neurocomputational nature of visual perceptual and higher-order cognitive abilities using neural oscillations and how they synchronize within and between cortical regions. The breadth of research topics, subject populations, and methods is also unique. We are currently conducting studies ranging from low vision (e.g., contrast sensitivity, 3D-shape perception via motion) to core cognitive functions (e.g., working memory maintenance, updating, gating, deletion; executive control; episodic long-term memory) to high-order, more complex processes (e.g., emotional memory, concept abstraction, creativity, consciousness). Our studies are conducted in healthy younger adults, healthy older adults, and people with neurodegenerative disorders (mild cognitive impairment, Alzheimer's disease) and neuropsychiatric disorders (schizophrenia, obsessive compulsive disorder). The methods we employ are also wide-ranging, as listed above, and we lean on our many collaborators when our research questions veer outside our core expertise (e.g., David Soto, consciousness; Andrew Budson, Alzheimer's disease; Matcheri Keshavan, schizophrenia; Sam Ling, fMRI low vision, to name a few). We seek individuals who enjoy working on challenging problems with enthusiasm and creative rigor in a collaborative team-based environment. This position is open to both US citizens and foreign nationals. Start date is flexible. The term of this appointment is two years with the possibility of renewal. Essential qualifications for this position include: a Ph.D. in Neuroscience, Computer Science, Bioengineering, Cognitive Science or other closely related fields. A background in electrophysiology of the visual system and computational-representational theories of mind is preferred. All candidates should possess strong quantitative skills (e.g. Matlab, C++, Python). To apply, email Rob Reinhart (rmgr(a)bu.edu) and include a cover letter, CV, research statement, and contact information for three references.

1 0

Re: [Freesurfer] if: Expression Syntax - preproc-sess
by Stefano Delli Pizzi 10 Mar '24

10 Mar '24

External Email - Use Caution Here -debug outputs preproc-sess -s 091223sbj01m_tp1 -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest -per-run -sliceorder up -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 ( 091223sbj01m_tp1 ) set tmp = ( ) ; set tmp = ( ) foreach d ( $SearchPathList ) foreach d ( . ) set stst = $d/$sess set stst = ./091223sbj01m_tp1 if ( -d $stst ) then if ( -d ./091223sbj01m_tp1 ) then if ( ! -r $stst ) then if ( ! -r ./091223sbj01m_tp1 ) then pushd $stst > /dev/null ; pushd ./091223sbj01m_tp1 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 = ( /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 ) end end set UniqueList = ( ) ; set UniqueList = ( ) foreach s ( $SessPath ) foreach s ( /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 ) 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 = ( /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 ) endif endif end end echo $SessPath echo /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 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 ( $#instem == 0 ) set instem = "f" ; if ( 0 == 0 ) set instem = f set instem = f if ( $#fsd == 0 ) then if ( 1 == 0 ) then if ( $DoMC || $DoReg ) then if ( 0 || 1 ) then if ( $PerRun == 0 && $PerSess == 0 ) then if ( 1 == 0 && 0 == 0 ) then endif endif if ( $DoMC ) then if ( 0 ) then set mcoutstem = $instem ; set mcoutstem = f endif endif if ( $DoSTC ) then if ( 1 ) then if ( $#stcinstem == 0 ) set stcinstem = $mcoutstem if ( 0 == 0 ) set stcinstem = f set stcinstem = f if ( $#stcoutstem == 0 ) then if ( 0 == 0 ) then if ( $#SliceOrder ) set stcoutstem = $stcinstem.$SliceOrder if ( 1 ) set stcoutstem = f.up set stcoutstem = f.up if ( $#SliceDelayFile ) set stcoutstem = $stcinstem.sdf if ( 0 ) set stcoutstem = f.sdf endif endif else else if ( $ToSurf || $ToMNI305 || $ToCVS ) then if ( 1 || 1 || 0 ) then if ( $#fwhm == 0 ) then if ( 1 == 0 ) then set DoVolSmooth = 0 ; set DoVolSmooth = 0 set DoSurfSmooth = 0 ; set DoSurfSmooth = 0 set DoSmooth = 0 ; set DoSmooth = 0 endif endif if ( $DoSmooth ) then if ( 0 ) then if ( $DoInorm && $#inormstem == 0 ) then if ( 0 && 0 == 0 ) then if ( ! $DoMC && ! $DoSTC && ! $DoSmooth && ! $DoMask && ! $DoTemplate ) then if ( ! 0 && ! 1 && ! 0 && ! 1 && ! 1 ) then if ( $#ProjFrac && $DoProjAvg ) then if ( 0 && 0 ) then if ( $UseB0DC && $#ProjFracExpKey ) then if ( 0 && 0 ) then if ( $#regfile == 0 ) then if ( 0 == 0 ) then if ( ! $UseB0DC ) set regfile = register.dof$RegDOF.lta if ( ! 0 ) set regfile = register.dof6.lta set regfile = register.dof6.lta if ( $UseB0DC ) set regfile = register.dof$RegDOF.b0dc.lta if ( 0 ) set regfile = register.dof6.b0dc.lta endif endif if ( $#SliceDelayFile != 0 && $#SliceOrder != 0 ) then if ( 0 != 0 && 1 != 0 ) then goto check_params_return ; goto check_params_return if ( $nolog ) then if ( 0 ) then set logdir = log ; set logdir = log mkdir -p $logdir mkdir -p log if ( ! -e $logdir ) then if ( ! -e log ) then if ( $#SessList > 1 ) then if ( 1 > 1 ) then set sb = `basename $SessList` set sb = `basename $SessList` basename /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 set LF = $logdir/preproc-sess.$sb.log set LF = log/preproc-sess.091223sbj01m_tp1.log endif endif if ( -e $LF ) mv $LF $LF.old if ( -e log/preproc-sess.091223sbj01m_tp1.log ) mv log/preproc-sess.091223sbj01m_tp1.log log/preproc-sess.091223sbj01m_tp1.log.old mv log/preproc-sess.091223sbj01m_tp1.log log/preproc-sess.091223sbj01m_tp1.log.old endif endif endif endif echo "--------------------------------------------------------------" echo -------------------------------------------------------------- -------------------------------------------------------------- echo "preproc-sess logfile is $LF" echo preproc-sess logfile is log/preproc-sess.091223sbj01m_tp1.log preproc-sess logfile is log/preproc-sess.091223sbj01m_tp1.log echo "--------------------------------------------------------------" echo -------------------------------------------------------------- -------------------------------------------------------------- echo "preproc-sess log file" >> $LF echo preproc-sess log file echo $VERSION | tee -a $LF echo FreeSurferEnv.csh 7.4.1 tee -a log/preproc-sess.091223sbj01m_tp1.log FreeSurferEnv.csh 7.4.1 echo "$user" | tee -a $LF echo stefano tee -a log/preproc-sess.091223sbj01m_tp1.log stefano echo "setenv FREESURFER_HOME $FREESURFER_HOME" | tee -a $LF echo setenv FREESURFER_HOME /Applications/freesurfer/7.4.1 tee -a log/preproc-sess.091223sbj01m_tp1.log setenv FREESURFER_HOME /Applications/freesurfer/7.4.1 echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF echo setenv SUBJECTS_DIR /Users/stefano/Desktop/MODAFINIL/MRI tee -a log/preproc-sess.091223sbj01m_tp1.log setenv SUBJECTS_DIR /Users/stefano/Desktop/MODAFINIL/MRI uname -a | tee -a $LF uname -a tee -a log/preproc-sess.091223sbj01m_tp1.log Darwin IMACSTEFANO01.local 21.6.0 Darwin Kernel Version 21.6.0: Mon Dec 19 20:44:01 PST 2022; root:xnu-8020.240.18~2/RELEASE_X86_64 x86_64 pwd | tee -a $LF pwd tee -a log/preproc-sess.091223sbj01m_tp1.log /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA echo $0 | tee -a $LF echo /Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess tee -a log/preproc-sess.091223sbj01m_tp1.log /Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess echo $inputargs | tee -a $LF echo -s 091223sbj01m_tp1 -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest -per-run -sliceorder up -debug tee -a log/preproc-sess.091223sbj01m_tp1.log -s 091223sbj01m_tp1 -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest -per-run -sliceorder up -debug date | tee -a $LF date tee -a log/preproc-sess.091223sbj01m_tp1.log Lun 26 Feb 2024 18:46:29 CET echo "instem $instem " | tee -a $LF echo instem f tee -a log/preproc-sess.091223sbj01m_tp1.log instem f echo "mc $DoMC $mcinstem $mcoutstem " | tee -a $LF echo mc 0 f tee -a log/preproc-sess.091223sbj01m_tp1.log mc 0 f echo "stc $DoSTC $stcinstem $stcoutstem" | tee -a $LF echo stc 1 f f.up tee -a log/preproc-sess.091223sbj01m_tp1.log stc 1 f f.up echo "sm $DoVolSmooth $sminstem $smoutstem " | tee -a $LF echo sm 0 tee -a log/preproc-sess.091223sbj01m_tp1.log sm 0 echo "mask $DoMask $maskstem" | tee -a $LF echo mask 1 brain tee -a log/preproc-sess.091223sbj01m_tp1.log mask 1 brain set ProjectDir = `pwd` ; set ProjectDir = `pwd` pwd set StartTime = `date` ; set StartTime = `date` date foreach sess ( $SessList ) foreach sess ( /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 ) set sessid = `basename $sess` ; set sessid = `basename $sess` basename /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 set sessparent = `dirname $sess` ; set sessparent = `dirname $sess` dirname /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 if ( -w . && $nolog != 1 ) then if ( -w . && 0 != 1 ) then mkdir -p log mkdir -p log set LF = $ProjectDir/log/preproc-$sessid-$fsd.log set LF = /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log rm -f $LF rm -f /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log else else echo "preproc-sess" >> $LF echo preproc-sess echo $sessid >> $LF echo 091223sbj01m_tp1 echo $VERSION >> $LF echo FreeSurferEnv.csh 7.4.1 uname -a >> $LF uname -a date >> $LF date pwd >> $LF pwd echo $inputargs >> $LF echo -s 091223sbj01m_tp1 -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest -per-run -sliceorder up -debug echo "ProjectDir $ProjectDir" >> $LF echo ProjectDir /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA if ( $DoTemplate ) then if ( 1 ) then set cmd = ( mktemplate-sess -s $sessid -d $sessparent -fsd $fsd -funcstem $instem ) set cmd = ( mktemplate-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -funcstem f ) if ( $#RunListFile ) set cmd = ( $cmd -rlf $RunListFile ) ; if ( 0 ) set cmd = ( mktemplate-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -funcstem f -rlf ) if ( $nolog ) set cmd = ( $cmd -nolog ) ; if ( 0 ) set cmd = ( mktemplate-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -funcstem f -nolog ) if ( $UpdateOnly ) set cmd = ( $cmd -update ) ; if ( 1 ) set cmd = ( mktemplate-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -funcstem f -update ) set cmd = ( mktemplate-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -funcstem f -update ) echo "$sessid Template -----------------------------" | & tee -a $LF echo 091223sbj01m_tp1 Template ----------------------------- tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log 091223sbj01m_tp1 Template ----------------------------- echo $cmd | & tee -a $LF echo mktemplate-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -funcstem f -update tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log mktemplate-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -funcstem f -update $cmd | & tee -a $LF mktemplate-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -funcstem f -update tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log Session: /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 ---------------- Lun 26 Feb 2024 18:46:29 CET Detected input format at nii.gz 091223sbj01m_tp1 Update not needed Run: 001 ---------------- Lun 26 Feb 2024 18:46:30 CET 091223sbj01m_tp1 001 Update not needed Run: 002 ---------------- Lun 26 Feb 2024 18:46:30 CET 091223sbj01m_tp1 002 Update not needed Run: 003 ---------------- Lun 26 Feb 2024 18:46:30 CET 091223sbj01m_tp1 003 Update not needed Lun 26 Feb 2024 18:46:30 CET mktemplate-sess completed if ( $status ) exit 1 ; if ( 0 ) exit 1 endif endif if ( $DoReg ) then if ( 1 ) then set cmd = ( register-sess -s $sessid -d $sessparent -fsd $fsd -delete-dat ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat ) set cmd = ( $cmd -dof $RegDOF -$contrast ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold ) if ( $#RunListFile ) set cmd = ( $cmd -rlf $RunListFile ) ; if ( 0 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -rlf ) if ( $PerRun ) set cmd = ( $cmd -per-run ) if ( 1 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run ) if ( $PerSess ) set cmd = ( $cmd -per-session ) if ( 0 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -per-session ) if ( $nolog ) set cmd = ( $cmd -nolog ) ; if ( 0 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -nolog ) if ( $UpdateOnly ) set cmd = ( $cmd -update ) ; if ( 1 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update ) if ( $UseB0DC ) set cmd = ( $cmd -b0dc ) if ( 0 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -b0dc ) if ( $InitCoReg ) set cmd = ( $cmd -init-coreg ) if ( 1 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg ) if ( $InitFSL ) set cmd = ( $cmd -init-fsl ) if ( 0 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg -init-fsl ) if ( $InitSPM ) set cmd = ( $cmd -init-spm ) if ( 0 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg -init-spm ) if ( $InitHeader ) set cmd = ( $cmd -init-header ) if ( 0 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg -init-header ) if ( $#IntermediateFSD ) set cmd = ( $cmd -bbr-int $IntermediateFSD $IntermediateStem ) if ( 0 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg -bbr-int ) if ( $#BBRXopts ) set cmd = ( $cmd -bbr-xopts $BBRXopts ) if ( 0 ) set cmd = ( register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg -bbr-xopts ) echo "$sessid Registration -----------------------------" | & tee -a $LF echo 091223sbj01m_tp1 Registration ----------------------------- tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log 091223sbj01m_tp1 Registration ----------------------------- echo $cmd | & tee -a $LF echo register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg $cmd | & tee -a $LF register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log -------------------------------------------------------------- register-sess logfile is /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/register-sess.091223sbj01m_tp1.log -------------------------------------------------------------- Lun 26 Feb 2024 18:46:30 CET setenv SUBJECTS_DIR /Users/stefano/Desktop/MODAFINIL/MRI cd /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA /Applications/freesurfer/7.4.1/fsfast/bin/register-sess -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -delete-dat -dof 6 -bold -per-run -update -init-coreg freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin IMACSTEFANO01.local 21.6.0 Darwin Kernel Version 21.6.0: Mon Dec 19 20:44:01 PST 2022; root:xnu-8020.240.18~2/RELEASE_X86_64 x86_64 Session: /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 ---------------- Lun 26 Feb 2024 18:46:30 CET /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 Run: 001 ---------------- Lun 26 Feb 2024 18:46:30 CET Update not needed Run: 002 ---------------- Lun 26 Feb 2024 18:46:30 CET Update not needed Run: 003 ---------------- Lun 26 Feb 2024 18:46:30 CET Update not needed Lun 26 Feb 2024 18:46:30 CET register-sess completed if ( $status ) exit 1 ; if ( 0 ) exit 1 endif endif if ( $DoMask ) then if ( 1 ) then set cmd = ( mkbrainmask-sess -maskstem $maskstem ) set cmd = ( mkbrainmask-sess -maskstem brain ) set cmd = ( $cmd -fsd $fsd ) set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest ) set cmd = ( $cmd -s $sessid -d $sessparent ) set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA ) if ( $PerRun ) set cmd = ( $cmd -per-run ) if ( 1 ) set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run ) set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run ) if ( $PerSess ) set cmd = ( $cmd -per-session ) if ( 0 ) set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -per-session ) if ( $#RunListFile ) set cmd = ( $cmd -rlf $RunListFile ) ; if ( 0 ) set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -rlf ) if ( $nolog ) set cmd = ( $cmd -nolog ) ; if ( 0 ) set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -nolog ) if ( $UpdateOnly ) set cmd = ( $cmd -update ) ; if ( 1 ) set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -update ) set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -update ) if ( $UseB0DC ) set cmd = ( $cmd -b0dc ) if ( 0 ) set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -update -b0dc ) if ( $RegDOF != 6 ) set cmd = ( $cmd -dof $RegDOF ) if ( 6 != 6 ) set cmd = ( mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -update -dof 6 ) echo "$sessid Mask ------------------------" | & tee -a $LF echo 091223sbj01m_tp1 Mask ------------------------ tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log 091223sbj01m_tp1 Mask ------------------------ echo $cmd | & tee -a $LF echo mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -update tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -update $cmd | & tee -a $LF mkbrainmask-sess -maskstem brain -fsd rest -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -per-run -update tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log ------------------------------------------------ /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 Lun 26 Feb 2024 18:46:30 CET 091223sbj01m_tp1 Update not needed for session-level mask 091223sbj01m_tp1 Update not needed for run 001 mask 091223sbj01m_tp1 Update not needed for run 002 mask 091223sbj01m_tp1 Update not needed for run 003 mask 091223sbj01m_tp1 Update not needed for run 001 meanval 091223sbj01m_tp1 Update not needed for run 002 meanval 091223sbj01m_tp1 Update not needed for run 003 meanval Lun 26 Feb 2024 18:46:31 CET mkbrainmask-sess done if ( $status ) exit 1 ; if ( 0 ) exit 1 endif endif if ( $DoMC ) then if ( 0 ) then if ( $DoSTC ) then if ( 1 ) then set cmd = ( stc-sess -i $stcinstem -o $stcoutstem -ngroups $nSliceGroups ) set cmd = ( stc-sess -i f -o f.up -ngroups 1 ) if ( $#SliceOrder ) set cmd = ( $cmd -so $SliceOrder ) if ( 1 ) set cmd = ( stc-sess -i f -o f.up -ngroups 1 -so up ) set cmd = ( stc-sess -i f -o f.up -ngroups 1 -so up ) if ( $#SliceDelayFile ) set cmd = ( $cmd -sdf $SliceDelayFile ) if ( 0 ) set cmd = ( stc-sess -i f -o f.up -ngroups 1 -so up -sdf ) set cmd = ( $cmd -s $sessid -d $sessparent -fsd $fsd ) set cmd = ( stc-sess -i f -o f.up -ngroups 1 -so up -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest ) if ( $#RunListFile != 0 ) set cmd = ( $cmd -rlf $RunListFile ) ; if ( 0 != 0 ) set cmd = ( stc-sess -i f -o f.up -ngroups 1 -so up -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -rlf ) if ( $nolog ) set cmd = ( $cmd -nolog ) ; if ( 0 ) set cmd = ( stc-sess -i f -o f.up -ngroups 1 -so up -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -nolog ) if ( $UpdateOnly ) set cmd = ( $cmd -update ) ; if ( 1 ) set cmd = ( stc-sess -i f -o f.up -ngroups 1 -so up -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -update ) set cmd = ( stc-sess -i f -o f.up -ngroups 1 -so up -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -update ) echo "$sessid STC -----------------------------" | & tee -a $LF echo 091223sbj01m_tp1 STC ----------------------------- tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log 091223sbj01m_tp1 STC ----------------------------- echo $cmd | & tee -a $LF echo stc-sess -i f -o f.up -ngroups 1 -so up -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -update tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log stc-sess -i f -o f.up -ngroups 1 -so up -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -update $cmd | & tee -a $LF stc-sess -i f -o f.up -ngroups 1 -so up -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -update tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log Lun 26 Feb 2024 18:46:31 CET /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA /Applications/freesurfer/7.4.1/fsfast/bin/stc-sess -i f -o f.up -ngroups 1 -so up -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -update FreeSurferEnv.csh 7.4.1 IMACSTEFANO01.local 091223sbj01m_tp1 ----------------- Lun 26 Feb 2024 18:46:31 CET -rw-r--r-- 1 stefano staff 19539533 8 Feb 09:29 /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/001/f.up.nii.gz -rwx------ 1 stefano staff 19504393 7 Feb 08:32 /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/001/f.nii.gz Update not needed -rw-r--r-- 1 stefano staff 19734829 8 Feb 09:29 /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/002/f.up.nii.gz -rwx------ 1 stefano staff 19701816 7 Feb 08:32 /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/002/f.nii.gz Update not needed -rw-r--r-- 1 stefano staff 20008834 8 Feb 09:29 /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/003/f.up.nii.gz -rwx------ 1 stefano staff 19975502 7 Feb 08:32 /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/003/f.nii.gz Update not needed Started at Lun 26 Feb 2024 18:46:31 CET Ended at Lun 26 Feb 2024 18:46:31 CET stc-sess Done if ( $status ) exit 1 ; if ( 0 ) exit 1 endif endif if ( $ToSurf ) then if ( 1 ) then set cmd = ( rawfunc2surf-sess -fwhm $fwhm ) set cmd = ( rawfunc2surf-sess -fwhm 0 ) set cmd = ( $cmd -s $sessid -d $sessparent -fsd $fsd ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest ) if ( "$hemi" == lh || "$hemi" == rh ) set cmd = ( $cmd -hemi $hemi ) if ( lhrh == lh || lhrh == rh ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -hemi lhrh ) if ( $subject == self ) set cmd = ( $cmd -self ) if ( fsaverage == self ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -self ) if ( $subject != self ) set cmd = ( $cmd -trgsubject $subject ) if ( fsaverage != self ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage ) if ( $#RunListFile != 0 ) set cmd = ( $cmd -rlf $RunListFile ) ; if ( 0 != 0 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -rlf ) if ( $#SliceOrder ) set cmd = ( $cmd -stc $SliceOrder ) if ( 1 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up ) if ( $#SliceDelayFile ) set cmd = ( $cmd -sdf $SliceDelayFile ) if ( 0 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -sdf ) if ( $nolog ) set cmd = ( $cmd -nolog ) ; if ( 0 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -nolog ) if ( $UpdateOnly ) set cmd = ( $cmd -update ) ; if ( 1 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update ) if ( $UseB0DC ) set cmd = ( $cmd -b0dc ) if ( 0 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -b0dc ) if ( $RegDOF != 6 ) set cmd = ( $cmd -dof $RegDOF ) if ( 6 != 6 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -dof 6 ) if ( $PerRun ) set cmd = ( $cmd -per-run ) if ( 1 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -per-run ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -per-run ) if ( $PerSess ) set cmd = ( $cmd -per-session ) if ( 0 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -per-run -per-session ) if ( $#ProjFrac ) set cmd = ( $cmd -projfrac $ProjFrac -expkey $ProjFracExpKey ) if ( 0 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -per-run -projfrac -expkey ) if ( $#volsurffwhm ) set cmd = ( $cmd -volsurffwhm $volsurffwhm ) if ( 0 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -per-run -volsurffwhm ) if ( ! $UseCortexLabel ) set cmd = ( $cmd -no-cortex-label ) if ( ! 1 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -per-run -no-cortex-label ) echo "$sessid To Surface -----------------------------" | & tee -a $LF echo 091223sbj01m_tp1 To Surface ----------------------------- tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log 091223sbj01m_tp1 To Surface ----------------------------- echo $cmd | & tee -a $LF echo rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -per-run tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -per-run $cmd | & tee -a $LF rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage -stc up -update -per-run tee -a /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log instem fmcpr.up outstem fmcpr.up.sm0.fsaverage.hemi ------------------------------ 1/1 091223sbj01m_tp1 1/1 091223sbj01m_tp1 001 lh --------- Lun 26 Feb 2024 18:46:32 CET /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/001/masks/brain.fsaverage.lh.pr.nii.gz does not need updating 1/1 091223sbj01m_tp1 002 lh --------- Lun 26 Feb 2024 18:46:32 CET /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/002/masks/brain.fsaverage.lh.pr.nii.gz does not need updating 1/1 091223sbj01m_tp1 003 lh --------- Lun 26 Feb 2024 18:46:32 CET /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/003/masks/brain.fsaverage.lh.pr.nii.gz does not need updating /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/masks/brain.fsaverage.lh.pr.nii.gz does not need updating 1/1 091223sbj01m_tp1 001 rh --------- Lun 26 Feb 2024 18:46:32 CET /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/001/masks/brain.fsaverage.rh.pr.nii.gz does not need updating 1/1 091223sbj01m_tp1 002 rh --------- Lun 26 Feb 2024 18:46:32 CET /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/002/masks/brain.fsaverage.rh.pr.nii.gz does not need updating 1/1 091223sbj01m_tp1 003 rh --------- Lun 26 Feb 2024 18:46:32 CET /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/003/masks/brain.fsaverage.rh.pr.nii.gz does not need updating /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/masks/brain.fsaverage.rh.pr.nii.gz does not need updating 1/1 091223sbj01m_tp1 001 lh --------- Lun 26 Feb 2024 18:46:32 CET ERROR: could not determine file for /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/001/fmcpr.up if ( $status ) exit 1 ; if ( 1 ) exit 1 exit 1 > Il giorno 23 feb 2024, alle ore 18:32, Stefano Delli Pizzi <sdellipizzi(a)gmail.com> ha scritto: > > Thank you! > I have already sent it to you (probabile to Yujing) some days ago. Were they not okay? > Could it be because I'm running data on MacOS? > If you do preprocessing with -nomc, does it work on your dataset? I've tried it with three different databases. > Regards > Stefano > >> Il giorno 23 feb 2024, alle ore 17:32, Douglas N. Greve <dgreve(a)mgh.harvard.edu> ha scritto: >> >> I cannot reproduce this locally. If you still want help, attach logs. You can also try running it with -debug as the first option and capture the copious terminal output. >> >> On 2/6/2024 8:39 AM, Huang, Yujing wrote: >>> Not sure where this happened. Does it produce any log files that you can share? Maybe both logs with and without the -nomc option. >>> >>> Best, >>> >>> Yujing >>> >>> From: freesurfer-bounces(a)nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Stefano Delli Pizzi >>> Sent: Saturday, February 3, 2024 2:33 PM >>> To: freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >>> Subject: [Freesurfer] if: Expression Syntax - preproc-sess >>> >>> External Email - Use Caution >>> >>> Hello FreeSurfer Developers, >>> I'm attempting to run preproc-sess with -nomc option >>> >>> preproc-sess -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest >>> -per-run -sliceorder up -force >>> if: Expression Syntax. >>> >>> This error occurred before to create the file with slice timing correction >>> >>> The error did not occur when I run the preproc-sess command line without the >>> -nomc option. >>> >>> I've searched the list and no similar errors have been reported. Does anyone >>> have any thoughts on how to trouble-shoot this one? >>> >>> FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 >>> Platform: Darwin Kernel Version 21.6.0 >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://secure-web.cisco.com/1RGtmPM0hlMCo8Zjca56xbEFgG_xp75QgnTr8BS72v1bhO… <https://secure-web.cisco.com/1RGtmPM0hlMCo8Zjca56xbEFgG_xp75QgnTr8BS72v1bhO…> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1RGtmPM0hlMCo8Zjca56xbEFgG_xp75QgnTr8BS72v1bhO… >> 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1c9_PdX0MS4Dp1t3_S7ig7NDDRwU6Z42WDROfxYfWwU2LW… <https://secure-web.cisco.com/1c9_PdX0MS4Dp1t3_S7ig7NDDRwU6Z42WDROfxYfWwU2LW…> .

2 6

Trouble Project Surface Annotation to Volume
by Bram Diamond 10 Mar '24

10 Mar '24

External Email - Use Caution Hello FreeSurfer Experts! I’m having trouble projecting the Yeo 17n annotation to volume space. I’ve tried on FS v7.4.1 on Mac OS (14.3.1) and FS v7.3.2 on Linux (7.9). I’ve tried the following two methods: ---- 1. aparc2aseg ---- cd $FREESURFER_HOME/subjects/fsaverage/label mri_aparc2aseg \ --s fsaverage \ --o Yeo2011_17Networks_N1000.mgz \ --annot Yeo2011_17Networks_N1000 ---- Output ---- SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects subject fsaverage outvol Yeo2011_17Networks_N1000.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.white Reading lh pial surface /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.pial Loading lh annotations from /Applications/freesurfer/7.4.1/subjects/fsaverage/label/lh.Yeo2011_17Networks_N1000.annot Have color table for lh white annotation Building hash of lh white Building hash of lh pial Reading rh white surface /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/rh.white Reading rh pial surface /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/rh.pial Loading rh annotations from /Applications/freesurfer/7.4.1/subjects/fsaverage/label/rh.Yeo2011_17Networks_N1000.annot Have color table for rh white annotation Building hash of rh white Building hash of rh pial Loading ribbon segmentation from /Applications/freesurfer/7.4.1/subjects/fsaverage/mri/ribbon.mgz Loading aseg from /Applications/freesurfer/7.4.1/subjects/fsaverage/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice (256) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 332584 Used brute-force search on 0 voxels Writing output aseg to Yeo2011_17Networks_N1000.mgz error: mghWrite(Yeo2011_17Networks_N1000.mgz, -1): could not open file #VMPC# mri_aparc2aseg VmPeak 0 mri_aparc2aseg done ---- 2. label2vol ---- cd $FREESURFER_HOME/subjects/fsaverage/label mri_label2vol \ --annot lh.Yeo2011_17Networks_N1000.annot \ --o lh.Yeo2011_17Networks_N1000.mgz \ --hemi lh \ --fill-ribbon \ --identity \ --subject fsaverage ---- Output ---- Number of labels: 0 Annot File: lh.Yeo2011_17Networks_N1000.annot Template Volume: (null) Outut Volume: lh.Yeo2011_17Networks_N1000.mgz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: fsaverage Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects 7.4.1 INFO: loading surface /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.white nvertices = 163842 Reading thickness /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.thickness Loading annotations from lh.Yeo2011_17Networks_N1000.annot annotidmax = 18 nlabels = 18 Loading /Applications/freesurfer/7.4.1/subjects/fsaverage/mri/ribbon.mgz Mapping error: mghWrite(lh.Yeo2011_17Networks_N1000.mgz, -1): could not open file ---- I’ve done this before, so I feel like I must be doing something wrong. Any ideas? Cheers, Bram Bram R. Diamond, MS Clinical Psychology Doctoral Candidate Northwestern University Feinberg School of Medicine Mesulam Center for Cognitive Neurology & Alzheimer’s Disease 300 E. Superior Street | Tarry 8 | Chicago, IL 60611 http://secure-web.cisco.com/1sXX_vt8lgAXmW5X0_GiTpKrZ-h1ollL1p35VMiSyPIOs3Z…

2 1

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