Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

How to get the difference between motion, NU intensity correction images and the originate image?
by chen 06 May '19

06 May '19

External Email - Use Caution Dear All, I ran recon-all using single MPRAGE data set. According to my results, there exsit difference between ROIs. So, i want to check the difference between the originate image and the images after motion and NU intensity correction to confirm the most variation area. How can i get this information?I am looking forward to your kind suggestions.Best regards,Jiachen ------------------ 首都医科大学宣武医院杜佳晨

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trac-all -bedp error
by Daniel Callow 06 May '19

06 May '19

External Email - Use Caution Hello, When running the pre.job script created from /Volumes/DANIEL/trac-all -bedp -jobs job -c /Volumes/DANIEL/ dmrirc.long.example.sh which I am trying to submit by running setenv FREESURFER_HOME /Applications/freesurfer/ source $FREESURFER_HOME/SetUpFreeSurfer.csh foreach subj (AES101 AES102 AES104 AES107 AES108 AES109 AES110 AES111) bedpostx_preproc.sh /Volumes/DANIEL/dti_freesurf/trac/Ex.${subj}.long.base_${subj}/dmri bedpostx_preproc.sh /Volumes/DANIEL/dti_freesurf/trac/Rest.${subj}.long.base_${subj}/dmri end end I get the following error. [255a-280:/Volumes/DANIEL/dti_freesurf] amos% ./pre.job.sh Copying files to bedpost directory usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory /usr/local/fsl/bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator expected Done Is this the incorrect way of trying to run trac-all -bedp in parallel? And if so how should I go about running the job scripts? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Volume computation from Surface and Thickness
by Daniela Vecchio 06 May '19

06 May '19

External Email - Use Caution Dear all, referring to the lh.aparc.DKTatlas40.stats Freesurfer output, I would like to know how the GrayVol column is computed as just multiplying ThickAvg*SurfArea I obtained different values. Thanks in advance for helping! Dani

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Transforming Amygdala nuclei atlas to MNI space
by Dev vasu 04 May '19

04 May '19

External Email - Use Caution Dear all, I am having a difficulty in transforming the segmented subfields of Amygdala atlas from surface based .mgz to nifti format. I have extracted the labels using mri_extract_label lh.hippoAmygLabels-T1.v21.nii.gz 7009 Cortico_amygloid.mgz then i convert .mgz file to NIFTI using mri_convert Cortico_amygloid.mgz Cortico_amygloid.nii.gz. Later i tried to transform Cortico_amygloid.nii.gz to MNI space using FLIRT but i notice seed region Cortico_amygloid.nii.gz is oriented in different place. Kindly let me know what more i have to do , in order to transform .mgz label into MNI space. Thanks Vasudev

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Petsurfer: Motion Correction
by Shane Schofield 04 May '19

04 May '19

External Email - Use Caution Hi Freesurfer Team, How may I align 5 volumes of my PET data ( 5 min acquisitions each) to a mean image for motion correction across the acquisition? I can use mri_concat to get the the mean image, but I am not sure how to do the realignment after that. Thank you. Best Wishes,Shane

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[WARNING: UNSCANNABLE EXTRACTION FAILED]Transforming Amygdala nuclei atlas to MNI space
by Dev vasu 03 May '19

03 May '19

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applyMorph on talairach.m3z
by Peled, Noam 03 May '19

03 May '19

Dear group, How can I apply the talairach.m3z transformation on a list of points? I was trying to use applyMorph on one of my subjects: applyMorph --template $SUBJECTS_DIR/M1/mri/orig.mgz --transform $SUBJECTS_DIR/M1/mri/transforms/talairach.m3z point_list $SUBJECTS_DIR/M1/electrodes/electrodes_to_morph.txt tal.txt a but I got this error: Template name:/autofs/space/thibault_001/users/npeled/subjects//M1/mri/orig.mgz After loading template Template name:/autofs/space/thibault_001/users/npeled/subjects//M1/mri/orig.mgz After loading template extension = m3z terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Abort (core dumped) I'm using the FreeSurfer dev version (in martinos), and my SUBJECT_DIR is /autofs/space/thibault_001/users/npeled/subjects/ Thanks! Noam

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recon-all error
by 王梦星 03 May '19

03 May '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attampting to do a structural MRI analysis with the command "recon-all -i sub102.nii.gz -s bert -all", as described in the FreeSurfer Download and Install (http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall) But I always met the error as recorded in the recon-all.log, " /home/share/test2/bert/surf mris_curvature -w lh.white.preaparc total integrated curvature = 10.012*4pi (125.809) --> -9 handles ICI = 164.9, FI = 1856.5, variation=28617.761 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux wmx 2.6.32-754.12.1.el6.x86_64 #1 SMP Tue Apr 9 14:52:26 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Mon Apr 22 11:44:12 CST 2019 " And then I checked that, the '?.white.preaparc' had been created while the '?h.white.H/K' had not, so I did some steps described in http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0, The commands "mris_curvature -w ?h.white.preaparc " and " mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated " were done to generate some files successfully. Howevere, when I continue to use "mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/?h.curv.stats -F smoothwm <subjid> ?h curv sulc ", there were errors below: " mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/?h.curv.stats -F smoothwm bert ?h curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/?h.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ bert/?h.smoothwm ] Reading surface...MRISread(/home/share/test2/bert/surf/?h.smoothwm): could not open file No such file or directory [ ok ] mris_curvature_stats: could not read surface file /home/share/test2/bert/surf/?h.smoothwm No such file or directory " In fact, the '?h.smoothwm' files exist and I can find it by 'ls' commond. Any help is greatly appreciated. Thanks. Mengxing Wang

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resampling to native space for recons with multiple T1s
by Zimmerman, Jared 02 May '19

02 May '19

External Email - Use Caution Hi Freesurfers, What’s the best way to resample recon data such as aparc+aseg.mgz into scanner space for recons with multiple T1s? Right now I’m using mri_vol2vol with –regheader to resample from orig space to rawavg, then using mri_vol2vol again with the 001.lta, 002.lta etc. registration matrices to get it back to the original scanner space for each T1. Is there a way to do this without two interpolation steps? Thanks, jared

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Failure to import cortical surface extracted with Freesurfer into Matlab using ft_read_headshape
by Darinka Trübutschek 02 May '19

02 May '19

External Email - Use Caution Dear freesurfer community, I am currently trying to import cortical surfaces extracted with freesurfer (version: freesurfer-linux-centos7_x86_64-dev-20190403-dacefd1) into Matlab (version: R2018b) using the fieldtrip function ft_read_headshape (version: 20190329). All of this is run in an Ubuntu 18.04.2 LTS environment. While all of the extracted surfaces seem fine upon visual inspection in freeview, the import into Matlab fails, throwing the following error message: pial = ft_read_headshape('freesurfer/surf/lh.pial'); Error using fread Invalid size. Error in read_surf (line 72) vertex_coords = fread(fid, vnum*3, 'float32') ; Error in ft_read_headshape (line 909) [pos, tri] = read_surf(filename); It is most certainly related to the fact that, both for the number of vertices (vnum) and the number of faces (fnum), the function read_surf returns non-sensible (?) values (i.e., vnum = -1.0263e+09 and fnum = -1.0529e+09). The same code produces no error when run on the same pial surface extracted with a different version of freesurfer (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) in a different Ubuntu environment (Ubuntu 16.04 LTS). As visual inspection in Freeview of the 2 surfaces from the two different Freesurfer versions reveals no obvious differences, I am therefore at a loss as where exactly to start to fix this problem and would be grateful for any help. Many thanks! Darinka -- Darinka Trübutschek, PhD Department of Experimental Psychology Anna Watts Building Radcliffe Observatory Quarter Woodstock Road Oxford, OX2 6GG UK website: https://sites.google.com/site/dtruebutschek/

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