Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

Merge Images
by Cleudiana Lima 08 Nov '17

08 Nov '17

Could you please help me with my problem? I have a Nifti image with segmented white matter hyperintensity and a wparc image made at freesurfer. I want to know how I can know the names of the Nifti image areas, using a wparc as a location map. So, the problem is: identify all areas. I wanted an automatic process that would carry out this evaluation generating volumetric data and the names of the regions of intersection between these two images. -- Cleudiana Lima

2 1

problems of testing freesurfer
by Danny Deng 08 Nov '17

08 Nov '17

Hi developers, I just installed the software and there are so many problems I wish to seek help from you when I tried “Test your freesurfer installation” on the website Example 2 I tried several commands as follow but all failed: 1. Xues-MacBook-Air:~ DannyDeng$ export SUBJECTS_DIR=<$FREESURFER_HOME/subjects/sample-001.mgz .> -bash: syntax error near unexpected token `newline’ 2. Xues-MacBook-Air:~ DannyDeng$ > export SUBJECTS_DIR=<cp $FREESURFER_HOME/subjects/sample-001.mgz .> -bash: syntax error near unexpected token `newline’ 3. Xues-MacBook-Air:~ DannyDeng$ >export SUBJECTS_DIR=<&FREESURFER_HOME/subjects/sample-001.mgz .> -bash: syntax error near unexpected token `newline’ 4. DannyDeng$ DannyDeng$SUBJECTS_DIR -bash: DannyDengcp/Applications/freesurfer/subjects/sample-001.mgz: No such file or directory Besides, I think I can’t find nifti file in my freesurfer folder. example 3 Same problem like example 2: Xues-MacBook-Air:~ DannyDeng$ export SUBJECTS_DIR=<cp $FREESURFER_HOME/subjects/sample-001.mgz.> -bash: syntax error near unexpected token `newline’ example 4: Only this one I successfully opened it. Thanks very much. Best Regards, Danny Deng

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freesurfer@nmr.mgh.harvard.edu
by aurelie ponz 08 Nov '17

08 Nov '17

Dear Freesurfer users, I have big issues performing recon-all into the freesurfer VirtualBox. I dont get any error but no files are created except the 0001.mgz. Here is what I get. WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux /usr/local/freesurfer/subjects/Groove_009 mri_convert /media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii /usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz mri_convert /media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii /usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w .nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0603182, -0.982945, 0.173726) j_ras = (-0.125291, 0.16521, 0.978268) k_ras = (0.990285, 0.0807736, 0.113189) writing to /usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz... Could you please help me I read ;ost threads and tried ;any solutions but I didnt found a solution, Many thanks in advance, Aurelie <http://cnec-projects.com>

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Registration
by N Saf 08 Nov '17

08 Nov '17

Dear Experts, In the volume-based stream, if I'm right the FreeSurfer does two registration with MNI305 ,one affine and one nonlinear , is it possible to perform the nonlinear registration somewhere else and then use the result in FreeSurfer and run the rest of the analysis ? thank's alot for your great support. BRG, Nazanin

2 3

Qdec result
by hiroki.sato＠med.tohoku.ac.jp 07 Nov '17

07 Nov '17

Dear experts I'm using Qdec. I want to check regions where age and thickness are correlated, and regions where the thickness-age correlation differ between genotype(Hetero or WT). When I choose "genotype(Hetero or WT)" as Fixed factors and "age" as Continuous variables, I can choice the results "Does the correlation between thickness and age, accounding for genotype, differ from zero" and "Does the thickness-age correlation differ between Hetero and WT?". I have two questions. Is "Does the correlation between thickness and age, accounding for genotype, differ from zero" equal to the results of "Does the correlation between thickness and age differ from zero" that I choose only "age" as Continuous variables? I don't know the meaning of "accounding for genotype" but these two results are almost same. Does just a little different results come from the difference of Degrees Of Freedom? Thank you in advance. Best, Hiroki

2 1

missing register.dof6.dat
by Guy Avraham 07 Nov '17

07 Nov '17

Hello Freesurfer developers, I was running FSFAST preprocessing: preproc-sess -s [subject] -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 0 -per-run The process finished without errors. However, the register.dof6.dat is missing from the subject's folder. I could not find any error in the register.dof6.dat.log file (see attached). - Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c - OS: Ubuntu 16.04 LTS - recon-all.log file is also attached. Thanks! Guy

2 1

cut-off clusters size
by stdp82＠virgilio.it 07 Nov '17

07 Nov '17

Hi, I wonder if there is a consensus to thershold the size of clusters obtained by FS-FAST after FDR correction?To cut-off clusters size>10-15 mm2 should be good? or do you advise more than? ThanksStefano

2 1

mask volume calculation
by Ehsan Tadayon 07 Nov '17

07 Nov '17

Hello FS experts, I'm trying to get the volume of a binary mask on orig.mgz. I know that FS uses a more sophisitcated approach than simply counting the number of voxels within the mask and I'd like to apply the same approach. Is there any way to get the volume for a defined mask with the same approach that FS computes the volumes for aseg.mgz? thanks. Ehsan ‌

5 4

mris_preproc srcsurfreg Freesurfer 6.0
by M del Mar Velasco 07 Nov '17

07 Nov '17

Dear FreeSurfer experts, I am using mris_preproc command with following options: mris_preproc --s s_001 --s s_002 --s s_003 --target my_subject_average --hemi lh --meas my_input_surf.mgh --out /my_output_path/output_file I observe mris_preproc uses mri_surf2surf. My question is related to Freesurfer version. Using FreeSurfer 5.3, mri_surf2surf takes sphere.reg as srcsurfreg, while with Freesurfer 6 script mri_surf2surf has changed. It takes my_subject_average.sphere.reg (target of mris_preproc) as srcsurfreg. I get an error because my_subject_average.sphere.reg file doesn't exist inside s_001 folder. Why Freesurfer 6 changes srcsurfreg to $target.sphere.reg? What can I do in order to be coherent with my script which was designed using Freesurfer 5.3? Thanks in advance, M del Mar

2 1

mri_cvs_register: how to read/import .m3z warp file
by Stefano Zappalà 06 Nov '17

06 Nov '17

Dear FreeSurfer Developers, I am trying to visualize and modify the output warp field (in .m3z) of a mri_cv_registration call aimed at aligning a T1w scan to the MNI space. I was wondering how file format .m3z is organized, in order to read it with, for example, matlab. Or if there are simpler file format to convert the warp field to. No information about it seems to be reported in the website. Moreover, I've searched the list and a similar question was not answered. I was wondering if you have some suggestions in reading the output warp field of mri_cvs_register. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: ubuntu 16.04 LTS Many thanks, Stefano.

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