Freesurfer August 2020

freesurfer@nmr.mgh.harvard.edu

101 participants
152 discussions

Curvature files in FreeSurfer: source surface?
by Tim Schäfer 06 Aug '20

06 Aug '20

External Email - Use Caution Dear FreeSurfer experts, I would like to know whether the mean curvature files generated by recon-all (at <subject>/surf/?h.curv and ?h.curv.fwhmxx.fsaverage.mgh) contain the curvature for the white or for the pial surface? Thanks, Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Help with LGI
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 05 Aug '20

05 Aug '20

External Email - Use Caution Dear Freesurfer experts, I'm needing some simple help running LGI. After downloading MATLAB + Image processing toolbox and double checking if the ?h.pial file is located in the SUBJECT_DIR, the recon-all -s (subject_ID) -localGI command still doesn't work. The output says that I still didn't install matlab onto my computer, so maybe it has something to do with setting $FREESURFER_HOME/matlab in your matlab path setup in your ~/matlab/starup.m script, but I'm unsure how to do this. Please see the output below: Mac-Pro:ace_complete ajobsaid$ recon-all -s HAR30003_srs2_2 -localGI Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b INFO: SUBJECTS_DIR is /Applications/ace_complete Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 ajobsaid 982768932 959822 Jul 9 10:50 /Applications/ace_complete/HAR30003_srs2_2/scripts/recon-all.log Darwin iMac-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64 x86_64 /Applications/ace_complete/HAR30003_srs2_2/mri/transforms /Applications/ace_complete/HAR30003_srs2_2 /Applications/ace_complete/HAR30003_srs2_2 #@# white curv lh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv Update not needed #@# white area lh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area Update not needed #@# pial curv lh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial Update not needed #@# pial area lh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial Update not needed #@# thickness lh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness Update not needed #@# area and vertex vol lh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness Update not needed #@# white curv rh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv Update not needed #@# white area rh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area Update not needed #@# pial curv rh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial Update not needed #@# pial area rh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial Update not needed #@# thickness rh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed #@# area and vertex vol rh Thu Jul 9 12:58:04 PDT 2020 cd /Applications/ace_complete/HAR30003_srs2_2/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed /Applications/ace_complete/HAR30003_srs2_2/surf #-------------------------------------------- #@# Local Gyrification Index lh Thu Jul 9 12:58:04 PDT 2020 \n mris_compute_lgi --i lh.pial \n ERROR: Matlab is required to run mris_compute_lgi! Darwin iMac-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64 x86_64 recon-all -s HAR30003_srs2_2 exited with ERRORS at Thu Jul 9 12:58:04 PDT 2020 Thanks, Alex

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mri_cvs_register for fMRI
by Peter Sperrer 05 Aug '20

05 Aug '20

External Email - Use Caution Dear FreeSurfer experts, My goal is to morph fMRI (data in voxel space) for best possible intersubject GM-overlap. I am using /mri_cvs_register/ as it seemed like a perfect tool for this. I have already run /recon-all /on the anatomical scan (160x239x200 voxels at 1x1x1mm) as well as /mri_cvs_register --mov [anatomical] --mni/. The resulting normalized brain (/final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz/) looks pretty good, maybe except for a remaining piece of skull, which does not seem to have impaired the brain data, though. // Functional data has been ST-corrected, realigned and coregistered to the anatomical data in SPM. Unfortunately, when I try to morph the fMRI images using /mri_vol2vol --mov [PreprocessedFunctional.nii] --o [MorphedPreprocessedFunctional.nii] --m3z cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z --noDefM3zPath --targ cvs/final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz/ I end up with a strangely distorted, cropped and ill-oriented image. The file size and resolution is also enormous. First of all, do you have any suggestions on what could have gone wrong? Is there a better way than using mri_cvs_register to normalize fMRI data so gyri and sulci between subjects match? Since I do not need such high resolution for smoothing and analysis, is there a better way than just down-sampling after the morph? Please excuse if any of these questions seem to have obvious answers to you, I am rather new to using FreeSurfer. I have already searched the mailing list archive and did not find a solution to my problem but only a slightly related problem from 2013 (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30673.html) In the solution it was also hinted that morphing fMRI data might be further supported in the future. Is there a tool or function which has been developed since then? I appreciate your advice! Thank you very much! Kind regards Peter Sperrer

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Local GI error
by Alexopoulos, Dimitrios 05 Aug '20

05 Aug '20

External Email - Use Caution We are getting an error running the -localGI utility on a subject. The screen output is below and the output recon-all log file is attached. Any help would be appreciated. Jim . . lGI for vertex number 4101 of the outer mesh is 1.4993 lGI for vertex number 4201 of the outer mesh is 0.6245 lGI for vertex number 4301 of the outer mesh is 0.97077 lGI for vertex number 4401 of the outer mesh is 1.5549 lGI for vertex number 4501 of the outer mesh is 0.57803 lGI for vertex number 4601 of the outer mesh is 5.1163. ... remeasuring lGI value for vertex iV = 4701. It may take a few minutes. WARNING -- Problem for vertex iV = 4701, lGI value is aberrantly high (lGI=23.2391)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. ERROR: compute_lgi did not create output file '/data/shimony/shimony2/neonatal/MOD1467_V1_a/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc' ! Linux linux1 3.10.0-514.10.2.el7.x86_64 #1 SMP Fri Mar 3 00:04:05 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s MOD1467_V1_a exited with ERRORS at Tue Aug 4 11:11:15 CDT 2020 For more details, see the log file /data/shimony/shimony2/neonatal/MOD1467_V1_a/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ________________________________ 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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Questions about speed up the longitudinal processing
by Yang Molly 05 Aug '20

05 Aug '20

External Email - Use Caution Hi list, I tried to run some longitudinal data with two time points with the latest version Freesurfer (7.1.0) on the Ubantu 16 system. "recon-all -base" with two time points need 5 hours to complete on my PC, and recon-all -long need 2 hours. I try to use the command "recon-all -long pre009 sub009base -parallel" and it went with errors. I was wondering if I can use other flags to speed up the recon-all -base and recon-all -long for each terminal. Thank you Molly

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Quetion about thalamic nuclei segmentation in freesurfer v7
by Haewon Roh 05 Aug '20

05 Aug '20

External Email - Use Caution Hi. I have a quetion about thalamic nuclei segmentation process in freesurfer v7. Now, I’ve got a large amounts of patients samples which were already pre-processed using “recon -all” pipeline in freesurfer version 6, but I want to know their specific volumes of thalamic nucleis or subsegmentations using freesufer 7. So, due to a quite large number of samples, I feel that it will take a very long time to do preprocessing again in freesurfer 7 and , if possible, without re-pre-processing in freesurfer v7.0, I’d like to do additional subsegmentation of thalamus as well as hippoamygdala. So I’ like to ask if these kinds of thalmic nuclei subsegmentaion or Hippo-amygdala subsegmentation which was newly-introduced in freesurfer 7.0, can be done using data which was pre-processed in freesurfer 6.0 already. (Is it possible to do thalamic segmentaiton using segmentThalamic nuclei pipeline in freesurfer 7 for the data already pre-processed in freesufer 6.0 ? ) and I am also very curious if their results will be different from the results which was made using only freesurfer v7 from pre-precessing? Best, H Roh.

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The input for Petsurfer
by Hengameh Marzbani 05 Aug '20

05 Aug '20

External Email - Use Caution Hello Freesurfer developers, I have PET images for brain and I want to analyze them with Petsurfer. But I don't have T1-weighted MRI of each subject. What should I do? Is it possible? Thank you in advance, Best regards, Hengameh

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Re: [Freesurfer] bad interpreter: No such file or directory error
by fsbuild 05 Aug '20

05 Aug '20

External Email - Use Caution Hello Hengameh, You probably need to install tcsh (and or csh). I would try, $ sudo apt-get install csh tcsh - R.. On Jul 30, 2020, at 09:19, Hengameh Marzbani <marzbani91(a)gmail.com> wrote:        External Email - Use Caution        Hello Freesurfer developers,I have installed FreeSurfer v7 on 2 machines running Ubuntu and made sure that the setting are fine. Also, freeview works by simply typing the freeview command.However,I have tried to run recon-all. but, I have got the following error message on all PCs:bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directoryalso The build-stamps.txt file contents:freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297bThank you in advance, Best regards, Hengameh_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Converting surface files to ASCII - order of vertices
by Walsh, Shane W. 04 Aug '20

04 Aug '20

Hi FreeSurfer community, I have a set of .mgh patch files that are mapped to the FsAverage4 atlas. I'd like to do some calculations on the xyz coordinates of the vertices that make up a patch. I've been able to get ahold of these xyz coordinates by using mris_convert to convert FsAverage4 surface files to ASCII. I want to ensure the validity of these calculations, and in that process, I've run into two questions: 1. Do the order of vertices in a surface file match that of a mris_convert'ed ASCII surface file? 2. Do the order of vertices in the patches match that of the mris_convert'ed ASCII file? In an attempt to answer to first question, I used Freeview to compare vertex coordinates in lh.inflated with lh.inflated.asc. I'm able to use Freeview to visualize the surface files and click on any vertex to get its xyz coordinates. However, the set of coordinates given in Freeview seems to be completely different than the set of coordinates given in the ASCII version of the surface file. I think this issue is best demonstrated by an example. If I load subjects/fsaverage4/surf/lh.inflated into Freeview, the first vertex (Vertex 0) is listed at [-36.79, -18.60, 64.82]. Not only is this coordinate different from the one on the first line of lh.inflated.asc, it's not contained anywhere in the file. I looked into if the the coordinates differ by a constant if we assume that they're listed in the same order in both files, but I found this not to be the case. Based on this information, I'm unsure of the answer to my first question. My suspicion is that there is some sort of transform applied to the coordinates. I feel like I would need to figure out the first question before I can answer the second. I've hit a dead end and any guidance on either question would be greatly appreciated. Thank you, Shane Walsh

1 0

using own skull stripped t1
by Julie Ottoy 04 Aug '20

04 Aug '20

External Email - Use Caution Dear freesurfer team I'm trying to use my own skull stripped T1 when running recon-all. For this, I'm doing following steps: 1) run recon-all with -autorecon-1 -noskullstrip 2) mri_convert --in_type nii --out_type mgz -rl ./FreeSurfer/ID/mri/orig.mgz -rt nearest ./own_skull_strip.nii.gz ./FreeSurfer/ID/mri/brainmask.mgz 3) run recon-all with -autorecon-2 and autorecon-3 My original own_skull_strip.nii.gz has matrix size 192x240x256. Therefore, when transforming to the size of brainmask.mgz (256x256x256), it deforms. I tried nearest, cubic, and interpolate, but none of them gives actually a good result in terms of retaining the contrast. I was wondering if it is important to keep a good contrast for brainmask.mgz , or whether this brainmask.mgz is just used to determine the brain borders for segmentation. (ie.: in which steps of recon-all is the brainmask.mgz actually used?) Any recommendations? Thank you! Julie

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Freesurfer August 2020