Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Volume timeseries to native and fsaverage
by özenç taskin 21 May '20

21 May '20

External Email - Use Caution Hello Freesurfer developers, I am trying to map a 4D volumetric EPI image between different surfaces and I'd like a little bit of guidance as I am slightly confused about some of the outputs of freesurfer. I have a preprocessed nifti EPI image in subject's anatomical space. First, I'd like to map this timeseries image to subject's native surface. Here is how I am currently doing this operation: 1 - Create a register.dat by using fsl identity matrix since I am already in the native space: tkregister2_cmdl --mov <epi> --fsl <ident.mat> --targ <rawavg.nii> --noedit --reg <register.dat> 2 - Then, using this register.dat to make surfaces from the 4D timeseries with: mri_vol2surf --mov <epi> --ref <anat> --reg <register.dat> --hemi lh --o <output_surface.mgz> I used these functions in the past to map statistical images to surface, but it might not be the right thing to do for timeseries in which case please let me know. Assuming this is correct though, next I want to move this native surface timeseries to fsaverage surface. I am pretty sure the calculations are in there, but I am not really sure which ones I need to use and with which freesurfer commands I can do this. Lastly, I came across this freesurfer page https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat which talks about fsaverage to native surface conversion and the examples there made me a bit confused. Aren't the surface files in the surf directory (e.g lh.pial, lh.inflated) already in the native space ? Do I need to create a lh.pial.native using these commands to overlay my timeseries image ? Best, Ozzy

3 5

qdec and mris_anatomical_stats help
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 21 May '20

21 May '20

External Email - Use Caution Dear Freesurfer experts, Hope everyone is doing well! Could someone please clarify some things about mris_anatomical_stats, done after running qdec + mapping label to all subjects? From what I can understand, the following code should be used: mris_anatomical_stats -l lh.supramarg.label \ -t lh.thickness -b -f 004/stats/lh.supramarg.stats 004 lh But if I created the ".label" file directly on qdec, by "mapping label to all subjects", and didn't use the mri_label2label code for "target subjects", how should I work around this to perform mris_anatomical_stat correctly? Also, I'm confused on when + where this "lh.thickness" file is created and stored. Please let me know if you need any other information about my code or my qdec output. Thank you, Alex Job Said

2 2

question on partial volume correction
by Barletta, Valeria 21 May '20

21 May '20

Dear Freesurfers, We need to analyze PET data after correcting for partial volume effect in the cortex, white matter and subarachnoid space. Is Freesurfer's partial volume correction working on all these areas or only the grey matter volume and surface? Is there a way to use gtmseg on the white matter and outside the pial surface? Thanks a lot, Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823

1 0

longitudinal trac -prep missing outputs
by Zeng, Qi 21 May '20

21 May '20

External Email - Use Caution Hi, I was running longitudinal trac-all. After the 3rd step -path was finished, I found that multiple pathways were missing (e.g. fminor). I traced back, realizing outputs from its first step trac-prep were missing corresponding pathways in SUBJ_base/dlabel/mni/fminor. However, the scripts of SUBJ_base_long_ses-1 and ses-2 both claimed "trac-preproc finished without error". I double checked the bval, bvec and DTI and increased the memory limit, the same problem still exists. So I was wondering how to fix it. Attached the compressed log file of SUBJ_base of trac -prep (too big). Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

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Re: [Freesurfer] Freesurfer version 7.0.0 and hippocampal segmentation
by Iglesias Gonzalez, Juan E. 20 May '20

20 May '20

Dear Vanessa, 1. No changes were made in the hippocampal module between 7.0 and 7.1, so you don’t need to rerun (as the subjects were reconned-all with 6.0, which doesn’t have any problems). 2. Yeah it may not be as easy to reproduce as running everything with the same version, but it’s perfectly fine to write in your paper that you reconned the brains with 6.0 and then processed the hippo and amygdala with 7.1. People (even reviewers!) understand that some labs don’t have the CPU cycles to quickly rerun all their data with FS every time a new version comes out. 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 Vanessa Cropley <vcropley(a)unimelb.edu.au> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, May 20, 2020 at 01:35 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Freesurfer version 7.0.0 and hippocampal segmentation External Email - Use Caution Hello Freesurfer team, I have just become aware of the release notes concerning v7.0.0 being recalled and not to be used, with the recommendation to use v7.1.0 instead: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes I have a couple of questions about the implications of this recall. We have processed a large dataset using freesurfer version 6, with all subjects being processed (recon-all) with the same version/platform. We would now like to segment the hippocampal subfields using the enhanced version of the module as outlined here: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields which requires Freesurfer 7. We have successfully run the hippocampal segmentation using freesurfer_v7.0.0_dev_20200405 (7.1 was not available at the time). My questions: 1. Given the recall of v7.0.0, does this mean that we should re-do the hippocampal segmentation that used v7.0.0 with v7.1.0? In other words, are all functions within v7.0.0 to be avoided, or just the recon-all stream? 2. Given that the recon-all was processed with v6, is it ok to perform the hippocampal subfield segmentation with v7? I understand that it is fine to perform post-processing functions outside the recon-all stream with newer versions (provided recon-all was done with the same version). Is my understanding correct? Thank you for your assistance. - Vanessa

2 1

recon-all -long erros
by Jieyin Feng 20 May '20

20 May '20

External Email - Use Caution Dear FreeSurfer experts, I am running longitudinal processing with FreeSurfer 7.1.0 on MacOX Catalina. The dataset is 5 time points with T1 data. I tried to run a single subject. So far it succeeded on Step 1 (recon-all at each time point), and Step 2 (-base to build the template), all of them reported successfully. But I failed at step3, recon-all -long, to compare each timepoint with the template. The log file is attached. I tried to run several times with different timepoints data, all reported the same stuff. My guess is at the last 9 row, reported that the cp command incorrectly. But I still have no idea to fix it, or maybe I need to go to freesurfer's script file? I have no idea... Thanks for you time and help in advance! Stay safe and sound! Best, Jieyin

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Re: [Freesurfer] Lazy Symbol binding errors
by fsbuild 20 May '20

20 May '20

External Email - Use Caution Hello Renxi, Did it not work to apply the patch we sent you via the information in a previous email ? - R. —- previous message —— You can try downloading and applying the FreeSurfer_6_0_0_Patch.zip file from here, https://drive.google.com/file/d/1ezjiNIbGNrNAiYD5ciYxMO2SK-R5vz9A/view?usp=… Open the archive and follow the instructions in README.patch file to replace the Freeview application and one of the libraries. ---- On May 20, 2020, at 16:49, RENXI LI <rli296(a)wisc.edu> wrote:        External Email - Use Caution        Hi,I have downloaded the FreeSurfer 6.0..0 from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/free… I still have a lazy symbol binding error as below:dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib  Expected in: /usr/lib/libSystem.B.dylibdyld: Symbol not found: ___emutls_get_address  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib  Expected in: /usr/lib/libSystem.B.dylibI also tried to update the binary folders using sudo -E fs_update,  but it gives me the following errors: (base) Renxis-Mac-mini:~ renxili$ sudo -E fs_updatePassword: Build is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c   Running this will update some of your freesurfer binaries. Shall I proceed? [y/n/Abort]: yrsync -zbrlv --progress --suffix=.1590006994_bak rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/* /Applications/freesurferreceiving file list ... rsync: change_dir "/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" (in pub) failed: No such file or directory (2)0 files to considersent 4 bytes  received 9 bytes  8.67 bytes/sectotal size is 0  speedup is 0.00rsync error: some files could not be transferred (code 23) at /BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-54/rsync/main.c(1404) [receiver=2.6.9] would you mind taking a look to see what might goes wrong?Best,Renxi_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Lazy Symbol binding errors
by RENXI LI 20 May '20

20 May '20

External Email - Use Caution Hi, I have downloaded the FreeSurfer 6.0.0 from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Dar… I still have a lazy symbol binding error as below: dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib I also tried to update the binary folders using sudo -E fs_update, but it gives me the following errors: (base) Renxis-Mac-mini:~ renxili$ sudo -E fs_update Password: Build is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Running this will update some of your freesurfer binaries. Shall I proceed? [y/n/Abort]: y rsync -zbrlv --progress --suffix=.1590006994_bak rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-D… /Applications/freesurfer receiving file list ... rsync: change_dir "/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" (in pub) failed: No such file or directory (2) 0 files to consider sent 4 bytes received 9 bytes 8.67 bytes/sec total size is 0 speedup is 0.00 rsync error: some files could not be transferred (code 23) at /BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-54/rsync/main.c(1404) [receiver=2.6.9] would you mind taking a look to see what might goes wrong? Best, Renxi

1 0

Re: [Freesurfer] Infant Freesurfer: infant_recon_all error {Disarmed}
by fsbuild 20 May '20

20 May '20

External Email - Use Caution I would check both csh and tcsh are installed with, $ which csh/bin/csh $ which tcsh/usr/bin/tcsh If not installed then do, e.g., for tcsh,$ sudo apt-get install  tcsh - subsequently the “which” command above should return the path to where it is on the system (if it was not installed). With the shells installed, you can also try running the script directly as an argument to a given shell, e.g. $ bash script <arguments> $ csh script <arguments> $ tcsh script <arguments> - R. On May 20, 2020, at 06:12, Fleur Warton <fleur.warton(a)gmail.com> wrote:        External Email - Use Caution        Hi,Thanks for the reply! The output for 'file' was tcsh. I switched to tcsh (just in that session) but got the same error when running infant_recon_all  if: Expression SyntaxKind regards,-- Fleur Warton Postdoctoral Research FellowDivision of Biomedical EngineeringFaculty of Health SciencesUniversity of Cape TownOn Wed, May 20, 2020 at 11:42 AM fsbuild <fsbuild(a)contbay.com> wrote:Hello Fleur,You should be able to do,$ file `which infant_recon_all`... and the output should tell you if it it is a csh script, a Bourne shell script, a binary, etc.Unless you explicitly made csh or bash your default shell, then at the dollar sign prompt the default shell in Ubuntu is "dash" and not bash or Bourne shell.   If the file command reports it's a Bourne shell then it might be a bash script.  Or a bash script with a hash bang line of /bin/sh will run using dash shell on Ubuntu and can exit with that error on bash syntax/grammar.  You can eliminate that possibility by first running bash, and then the script,$ bash$ infant_recon_all --s SUBJ --age AGE(with I presume arguments substituted for SUBJ and AGE)- R.Fleur Warton  May 20, 2020 at 04:05        External Email - Use Caution        Hi,I recently installed the Infant FreeSurfer package. When I try to run infant_recon_all (specific command: infant_recon_all --s SUBJ --age AGE) I get the error if: Expression SyntaxI tried switching shells from bash to tcsh but got the same error.The FreeSurfer version is freesurfer-infant-20200205My platform is Ubuntu 18.04Any suggestions how to fix this?Kind regards,Fleur _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

error in longitudinal processing recon-all -long
by Jieyin Feng 20 May '20

20 May '20

1 0

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