Freesurfer April 2020

freesurfer@nmr.mgh.harvard.edu

101 participants
170 discussions

mri_anatomical_stats - multiple subjects
by s7675854＠stud.uni-frankfurt.de 20 Apr '20

20 Apr '20

External Email - Use Caution Dear Freesurfer experts, I am trying to extract values within a ROI/label that I drew myself and registered to the subjects using mri_label2label. - is there a way to use mri_anatomical_stats for multiple subjects, so that the table output contains ROI information on all subjects and not only one (similar to e.g. aparcstats2table)? - It seems like I could use this command to extract information on e.g. thickness and surface area, but could I also use it for LGI data? (And if not, is there a different option for this measure?) Thanks a lot, Doro

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recon-all in 7.0.0-beta: /usr/bin/time not installed on server, failed many hours into run
by Renner, Brian 20 Apr '20

20 Apr '20

External Email - Use Caution Hello all! A cautionary tale between versions 6.0.0 and 7.0.0. I was running recon-all as I was with version 6.0.0 and found that my runs would fail on our hpc after failing to find /usr/bin/time. This would leave it in "is-running" state. I am currently awaiting the installation of the standalone /usr/bin/time on our server and will run recon-all to see if this resolves the issue. Attached is the full log, ending with the hard exit error. Best. BR -- Brian Renner, MD Research Associate, Neurology brian.renner(a)cshs.org<mailto:brian.renner@cshs.org> Cedars-Sinai 127 S. San Vicente Blvd, Suite A6600 : Los Angeles CA 90048 office 310-423-1589 : mobile 310-658-3492 : cedars-sinai.org<https://www.cedars-sinai.org/> IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is strictly prohibited. Thank you for your cooperation.

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Most effective way to compute stats/aseg.stats
by Ерохин Александр 19 Apr '20

19 Apr '20

External Email - Use Caution Hello together, Could you please suggest the most effective way (in terms of time) for computation of statistics on segmented volumes from .nii source file? So far I went though the following steps: recon-all -autorecon1 -no-isrunning -subjid test recon-all -gcareg -no-isrunning -subjid test recon-all -canorm -no-isrunning -subjid test And seem to be stuck on -careg as transforms/talairach.m3z is needed to proceed. As far as I can tell — there is no way around recon-all -careg which seems to be the most time consuming in the chain of invocations based on Step-wise Directives ( https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all) But I might be wrong and hoping for your expertise here. Many thanks, Aleksandr Erokhin.

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Data on the Freesurfer surface
by Mason Wells 18 Apr '20

18 Apr '20

External Email - Use Caution Hi all, I am trying to use an analysis package that works on surface based data (SamSrf). I have ran Feat and have a filtered_func file which is of course the motion corrected/unwarped version of my EPI. However, I need some advice on how to get these data onto the Freesurfer surface. I have found this page<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer>, but I wanted to double check this is the most up-to-date pipeline. On the page it suggests using the same DOF as used in Feat, I use BBR so this seems a little redundant. Has anyone on these lists got any experience of getting filtered_func onto the Freesurfer surface? Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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Re: [Freesurfer] Trac-All Error
by Hua, Jessica 17 Apr '20

17 Apr '20

External Email - Use Caution Hi Dr. Yendiki, Thanks! That fixed the issue I was having. Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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eTIV vs. manual ICV
by Alexopoulos, Dimitrios 17 Apr '20

17 Apr '20

External Email - Use Caution I was just wondering if using the eTIV from FS 6.0 is a reliabile measure for intracanial volume normalization. Typically, manual ICV includes extra-axial CSF which I don't think is included in the eTIV method, correct? Our population is a control adoloscent cohort and we are interested in global GM and WM, and cortical aparc volumes. Sent from Outlook Mobile<https://aka.ms/blhgte> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] -bash: segmentThalamicNuclei.sh: command not found
by Iglesias Gonzalez, Juan E. 17 Apr '20

17 Apr '20

Hi Veronica Did you source FreeSurfer? After that, the command would be: segmentThalamicNuclei.sh A7 /Users/vp/freesurfer/ANALISI_DATA/ Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Parisi Veronica <parisi.veronica(a)hsr.it> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, April 17, 2020 at 20:08 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] -bash: segmentThalamicNuclei.sh: command not found External Email - Use Caution Dear Freesurfer Support Team, I'm trying to run the segmentThalamicNuclei.sh to segment the thalamic nuclei on a subject. I am using the latest Freesurfer dev version (https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/) I previously ran recon-all to generate the required files for the thalamic segmentation tool using the version freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg<https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Dar…>. After the download of the dev version, I followed the http://freesurfer.net/fswiki/ThalamicNuclei?action=fullsearch&context=180&v… instruction as reported: - export FREESURFER_HOME=/Users/vp/freesurfer - cd $FREESURFER_HOME - curl "https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&d…" -o "runtime.tar.gz" - tar xvf runtime.tar.gz - rm $FREESURFER_HOME/runtime.tar.gz - segmentThalamicNuclei.sh bert [SUBJECTS_DIR] = segmentThalamicNuclei.sh A7 /Users/vp/freesurfer/ANALISI_DATA/A7/mri/norm.mgz However, the program exits with the following error message: -bash: segmentThalamicNuclei.sh: command not found It doesn't seem to me that there are errors in the paths. What can I do to fix the problem? Thank you, VP Rispetta l’ambiente: non stampare questa mail se non è necessario. Respect the environment: print this email only if necessary.

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-bash: segmentThalamicNuclei.sh: command not found
by Parisi Veronica 17 Apr '20

17 Apr '20

External Email - Use Caution Dear Freesurfer Support Team, I'm trying to run the segmentThalamicNuclei.sh to segment the thalamic nuclei on a subject. I am using the latest Freesurfer dev version (https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/) I previously ran recon-all to generate the required files for the thalamic segmentation tool using the version freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg<https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Dar…>. After the download of the dev version, I followed the http://freesurfer.net/fswiki/ThalamicNuclei?action=fullsearch&context=180&v… instruction as reported: - export FREESURFER_HOME=/Users/vp/freesurfer - cd $FREESURFER_HOME - curl "https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&d…" -o "runtime.tar.gz" - tar xvf runtime.tar.gz - rm $FREESURFER_HOME/runtime.tar.gz - segmentThalamicNuclei.sh bert [SUBJECTS_DIR] = segmentThalamicNuclei.sh A7 /Users/vp/freesurfer/ANALISI_DATA/A7/mri/norm.mgz However, the program exits with the following error message: -bash: segmentThalamicNuclei.sh: command not found It doesn't seem to me that there are errors in the paths. What can I do to fix the problem? Thank you, VP Rispetta l'ambiente: non stampare questa mail se non è necessario. Respect the environment: print this email only if necessary.

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Re: [Freesurfer] Does FS guarantee the same results if run several times?
by Xiaojiang Yang 17 Apr '20

17 Apr '20

External Email - Use Caution Thank you Douglas! In my case, two runnings were from Centos7 and Redhat7 respectively. Good thing is that the difference of the average thickness is small - it's 0.006 mm. Both lh and rh have 0.006 mm differences, but one's lh is thicker than the other's, while its rh is thinner than the other's. Xiaojiang

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Re: [Freesurfer] Does FS guarantee the same results if run several times?
by Xiaojiang Yang 17 Apr '20

17 Apr '20

External Email - Use Caution Hi Douglas, I checked the recon-all.log files for both, and found the difference - my mistake, one used FLAIR as extra input and the other did not. I did find another case that has two different results in two runnings. Both runnings have MPRAGE and FLAIR as inputs, but one of the runnings has used the option "-openmp 16", and the other did not. Also, the two runnings were from two different machines. What do you think is the factor that has caused the different results, the openmp or different machine? The FS on two machines are the same version (V6). Thanks! Xiaojiang

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Freesurfer April 2020