Freesurfer

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FreeSurfer questions exchange
by 刘亚飞 18 Aug '21

18 Aug '21

External Email - Use Caution Hello! In the process of learning freeSurefer, I have two questions: The first question is that I want to convert a file in .stl format to a .pial file, but the error "does not apear to be an STL file" appears when using the mris_convert command, and I confirm that my stl file path is Accurate, do you know how to convert stl files to pial files? The second question is how to use freesurfer to perform cortial surface parcellation with only .pial files? Thank you！

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Unsubscribe
by Rollo, Patrick 17 Aug '21

17 Aug '21

External Email - Use Caution I've tried several times to unsubscribe from the mailing list. Please help, I'm inundated with emails that are no longer relevant to me.

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LGI - trouble creating output file for each subject
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 17 Aug '21

17 Aug '21

External Email - Use Caution Hello again FreeSurfer experts, I am having some issues creating the output file with the LGI data for each subject. Could you please help me with this? See below the code (in bold) that I used and the outputs that I got. Please let me know if you need additional information! *mri_segstats --annot DCNL-fBMI-001_Siemens_MPRAGE rh aparc --i $SUBJECTS_DIR/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.pial_lgi --sum rh.DCNL_001_aparc.pial_lgi.stats* 7.1.0 cwd cmdline mri_segstats --annot DCNL-fBMI-001_Siemens_MPRAGE rh aparc --i /Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.pial_lgi --sum rh.DCNL_001_aparc.pial_lgi.stats sysname Darwin hostname CCAPSY-0GYM0XV machine x86_64 user ajobsaid whitesurfname white UseRobust 0 Constructing seg from annotation error: No such file or directory error: MRISread(/Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.white): could not open file The lh or rh.pial_lgi file is located in the surf folder in each subject. Should I transfer them to the stats folder and try something like *asegstats2table -s subjectID --statsfile=rh.pial_lgi --meas mean --tablefile SubjectID_rh_lgi_final.txt ? * Thank you so much!!

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Re: [Freesurfer] Setting up Freesurfer
by fsbuild 17 Aug '21

17 Aug '21

External Email - Use Caution Hello Haley, You could try bringing up a new terminal window and then do the following, $ cd $HOME$ bash… output deleted …$ export FREESURFER_HOME=/Applications/freesurfer/7.1.1 The ls command below should show you the two .sh files needed to setup the environment.  If you don’t see those two files listed, then something is likely wrong with the installation and you could try re-installing freesurfer (see download links at the end of this message). $ ls -l $FREESURFER_HOME/*Surfer*.sh-rwxr-xr-x  1 root  wheel  18223 Aug 11  2020 /Applications/freesurfer/7.1.1/FreeSurferEnv.sh* -rwxr-xr-x  1 root  wheel   1350 Aug 11  2020 /Applications/freesurfer/7.1.1/SetUpFreeSurfer.sh* Check you can read both of those files with the head command, $ head -1 $FREESURFER_HOME/FreeSurferEnv.sh#!/bin/bash -p $ head -1 $FREESURFER_HOME/SetUpFreeSurfer.sh#!/bin/bash -p If you don’t see that output from the head command for the first line in each file, then there could be a permission error.  In that case you could try manually setting the permissions with the chmod command,$ sudo chmod 755  $FREESURFER_HOME/FreeSurferEnv.sh$ sudo chmod 755  $FREESURFER_HOME/SetUpFreeSurfer.sh Then try the "head -1" command again to test reading the first line in each file. If the above all worked, then try source’ing the SetUpFreeSurfer.sh file (which in turn runs the FreeSurferEnv.sh file that you reported could not be found),$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.1.1 FSFAST_HOME       /Applications/freesurfer/7.1.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.1.1/subjects MNI_DIR           /Applications/freesurfer/7..1.1/mni If you need to re-install 7.1.1 for MacOS, the link for that is here, https://secure-web.cisco.com/1bISb5L_RaO9qHLk_GCjwJOWorsxrzGoSJ2… If you don’t need to continue to work with the 7.1.1 release, you could try the newer 7.2.0 release.  You can have both 7.1.1 and 7.2.0 installed and set FREESURFER_HOME to point to either one of them.  The link for the 7.2.0 release for MacOS is,https://secure-web.cisco.com/1zRdDSXh-D1BWJw53Mbc6pYU1EIIskfcqIPD-acokQW… You need admin/root privileges to run the .pkg installer files. - R. On Aug 17, 2021, at 17:41, Haley Park <hparkit(a)gmail.com> wrote:        External Email - Use Caution        Hello,I was able to run Freesurfer before but when I try to source it now with the codesource $FREESURFER_HOME/7.1.1/SetUpFreesurfer.shI get the message:/Applications/freesurfer/7..1.1/SetUpFreeSurfer.sh:source:42: no such file or directory: /Applications/freesurfer/FreeSurferEnv.shBut I do see that file in the directory in Finder.Any ideas?Thank you,Haley_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FSFAST (mkcontrast-sess) with Octave
by Lauri Tuominen 17 Aug '21

17 Aug '21

External Email - Use Caution Dear Surfers, I am trying to run fsfast mkcontrast-sess with octave. I used the following command: "mkcontrast-sess -analysis ../mkanalysis/ftap.sm05.lh -contrast ftap -a 1 -octave" I get the output below. I wonder if you could help me out? Am I missing a file or a path? Thank you so much Lauri Tuominen INFO: Found 2 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 1.00000000000000000000 0 mkcontrast2 -config ../mkanalysis/ftap.sm05.lh/ftap.config -anadir ../mkanalysis/ftap.sm05.lh -wcond 1.00000000000000000000 0 -sumconds -o ../mkanalysis/ftap.sm05.lh/ftap.mat -prestim 0 -wdelay 1 -octave mkcontrast2 7.1.1 cmtxfile ../mkanalysis/ftap.sm05.lh/ftap.mat nconds 2, wcond 1.00000000000000000000 0 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau cmtxfile ../mkanalysis/ftap.sm05.lh/ftap.mat monly 0 NCond 2 WCond 1.00000000000000000000 0 NDelay 1 WDelay 1 TER 0.050000 sumconds 1 sumdelays 0 nircorr 0 TPreStim 0 RmPreStim 0 rdelta 0 0 rtau 0 0 ndelays 1 CNorm 1 setwdelay 0 setwcond 0 Matlab file is /tmp/mkcontrast2.28236.m ------- octave output -------------------- error: 'mkcontrast2m' undefined near line 1, column 1 Tue 17 Aug 2021 15:04:43 EDT

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Setting up Freesurfer
by Haley Park 17 Aug '21

17 Aug '21

External Email - Use Caution Hello, I was able to run Freesurfer before but when I try to source it now with the code source $FREESURFER_HOME/7.1.1/SetUpFreesurfer.sh I get the message: /Applications/freesurfer/7.1.1/SetUpFreeSurfer.sh:source:42: no such file or directory: /Applications/freesurfer/FreeSurferEnv.sh But I do see that file in the directory in Finder. Any ideas? Thank you, Haley

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longitudinal LME stats
by Erik O'Hanlon 17 Aug '21

17 Aug '21

External Email - Use Caution Dear FS experts, I have run the longitudinal pipeline on a dataset with three timepoints. I am particularly interested in the longitudinal hippocampal and amygdala data and want to run LME on these. I've made the qdec table with the id age, sex and time between scans etc. and have exported all the hippocamapal and amygdala volumes to csv files to merge with demographic data. Should I smooth the hippocampal and amygdala measures before running the LME? Do I run Qcache and if so do I use recon-all -long SubID_tp1 subIDbase -qcache In the LME wiki instructions it gives an example for the mass-univariate approach on thickness. Is the study_average referring to the fsaverage ? Should I be using the ICV from the cross-sectional runs or the ICV measures in the "long" folders which refer? Thanks and any help is very much appreciated. Erik

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bbregister on DWI volumes using DOF 12 for epi distortions ?
by Shane Schofield 17 Aug '21

17 Aug '21

External Email - Use Caution Hi Freesurfer Experts, I am trying to obtain coregister diffusion data b0 with T1. One problem is that I do not have any means to correct for EPI distortions. Because of this, I am experimenting with DOF = 9 and DOF = 12. The mincost for 12 was consistently the lowest compared to 6 and 9 across my datasets [DOF 6 = 0.23, DOF 9 = 0.22, DOF 12 = 0.19]. However, it is hard to tell that DOF 12 is the best just by looking at the coregistered B0s overlaid on the brainmask. Would it be fine to proceed with the DOF 12 option? Thank you. Best Wishes,Shane

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Fwd: Base correction, longitudinal analysis
by Eszter Boros 17 Aug '21

17 Aug '21

External Email - Use Caution Dear FreeSurfer Team, I am working on a longitudinal pipeline and after correcting the Cross and generating the Base, I can still see some pial problems sometimes (on the Base). I read on the Freesurfer website that it is possible to correct and regenerate only the Base, but when I use this command: recon-all -base OAS2_0057 -autorecon-pial /where OAS2_0057 is the name of the Base/ I get the following error message: ERROR: must specify subjects for base subject using -base-tp Why is this not working? I am using Freesurefer 7.1.1. Thank you so much! All the best, Eszter Boros

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qcache option for post recon-all longitudinal data
by Zeng, Qi 17 Aug '21

17 Aug '21

External Email - Use Caution Hi Freesurfer experts, I've done running a longitudinal analysis pipeline for individuals in 3 groups. Now, I need to get prepared for QDEC group analysis. I cp all groups of individuals to the same directory and each subject contains one base and multiple long files. I want to run "-qcache" option for the prep. Got a couple of questions here? 1) I failed to run "recon-all -s 001 -qcache", said: "missing 001/surf/lh.thickness", so for a longitudinal run, should I run "recon-all -s 001_base -qcache" or 'recon-all -s 001_ses-1.long.001_base" instead? 2) Where will the output be stored for each individual? 3) To run multiple qcache in parallel, will the following code generate the same outputs as that I run each individually: " find . -type d -name '*_base" -exec bash -c 'for i in "$@"; do recon-all -s "$i" -qcache; done". Thank you so much! Best, Qi

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