Freesurfer

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30084 discussions

Cannot execute Binary file
by Graduate Imaging 30 May '20

30 May '20

External Email - Use Caution Hi, I recently downloaded fspalm, mri_surfcluster and mri_volcluster for freesurfer v6.0 from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/PALM/ and added them to the freesurfer/bin folder (had to replace the previous versions of mri_surcluster and mri_volcluster) and ran chmod a+x on all three to make them unix executable files. When I ran fspalm the permutation part of the command worked however when it reached the mri_surfcluster command it produced the following error in terminal "-bash:/Applications/freesurfer/bin/mri_surfcluster: cannot execute binary file" I'm running freesurfer on a MacOS system, are these the correct versions of the files I should be using? Thanks

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Re: [Freesurfer] Cannot execute Binary file {Disarmed}
by fsbuild 30 May '20

30 May '20

External Email - Use Caution Hello, The files mri_surcluster and mri_volcluster that you downloaded are patched versions for the linux distribution, so they won’t run on MacOS. But you should need to download them as they should already exist in the MacOS freesurfer distribution.  Or you should already have them under ./freesurfer/bin ($FREESURFER_HOME/bin in the freesurfer shell/environment) - under wherever your MacOS installation of freesurfer lives.   If you need to, you can download the freesurfer 6 MacOS distribution from https://surfer.nmr.mgh.harvard.edu/fswiki/rel6downloads, install it on your own Mac and get those files. - R. On May 29, 2020, at 23:20, Graduate Imaging <graduate.imaging(a)gmail.com> wrote:Hi, I recently downloaded fspalm, mri_surfcluster and mri_volcluster for freesurfer v6.0 from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6..0.0-patch… added them to the freesurfer/bin folder (had to replace the previous versions of mri_surcluster and mri_volcluster) and ran chmod a+x on all three to make them unix executable files. When I ran fspalm the permutation part of the command worked however when it reached the mri_surfcluster command it produced the following error in terminal "-bash:/Applications/freesurfer/bin/mri_surfcluster: cannot execute binary file" I'm running freesurfer on a MacOS system, are these the correct versions of the files I should be using? Thanks

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AAL parcellation for Freesurfer
by Bastian Cheng 29 May '20

29 May '20

External Email - Use Caution Dear all, does anyone know if there is a surface parcellation file based on the AAL for freesurfer? I am aware that I could recon-all the MNI brain and project the atlas on the surface. (but maybe someone already did that) I spend some time googeling this, but haven't found it, therefore my question. all the best, Bastian <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virenfrei. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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mri_cnr label flag
by Pradyumna Bharadwaj 29 May '20

29 May '20

External Email - Use Caution Hi, I had a question about the -label flag in mri_cnr. 1) When you do not use the -label option and just use the following command: mri_cnr $FREESURFER_HOME/subjects/bert/surf $FREESURFER_HOME/subjects/bert/mri/norm.mgz The output is as follows white = 96.6+-6.0, gray = 75.7+-13.5, csf = 55.3+-16.6 gray/white CNR = 1.983, gray/csf CNR = 0.907 lh CNR = 1.445 white = 96.4+-6.0, gray = 76.0+-13.3, csf = 55.6+-16.2 gray/white CNR = 1.952, gray/csf CNR = 0.943 rh CNR = 1.448 total CNR = 1.446 2) When you add -label $FREESURFER_HOME/subjects/bert/label/lh.cortex.label $FREESURFER_HOME/subjects/bert/label/rh.cortex.label to the first command, you get different (lower) cnr values. white = 96.6+-6.0, gray = 73.1+-18.9, csf = 50.8+-20.5 gray/white CNR = 1.389, gray/csf CNR = 0.644 lh CNR = 1.016 white = 96.4+-6.0, gray = 73.4+-18.8, csf = 51.0+-20.3 gray/white CNR = 1.353, gray/csf CNR = 0.652 rh CNR = 1.002 total CNR = 1.009 How is the lh.cortex and rh.cortex label changing the CNR computation? Any inputs or thoughts on this matter are greatly appreciated! Thanks, Prad

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Fwd: Error in Monte Carlo simulation
by behzad sorouri khorashad 29 May '20

29 May '20

External Email - Use Caution TO: freesurfer(a)nmr.mgh.harvard.edu SUBJECT: Error in Monte Carlo simulation: Error running mri_surfcluster Hello FreeSurfer Developers, I'm attempting to run a longitudinal analysis on structural T1 images for a sample, as described on the freesurfer wiki tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) For post processing data, i used qdec option. However, when i want to use the monte carlo correction I receive the following Error: Error in Monte Carlo:Error in running mri_surfcluster If I change the number in /qdec/untitlted/fwhm.dat to the fwhm i have chosen in my analysis, the error is solved. But I wonder whether this is correct way to solve this error or not. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the error in the terminal in case it's of any use. 1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0-2beb96c 2) Platform: OS X ElCapitan verson 10.11.6 Thanks for your help Yours Behzad

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dimension mismatch longitudinal
by KennethSPrice 28 May '20

28 May '20

External Email - Use Caution Hello Freesurfers! In regards to the link below: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36839.html Is there a way to fix a dimension mismatch? Thanks, Ken Sent with [ProtonMail](https://protonmail.com) Secure Email.

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Re: [Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs
by Marina Fernández 28 May '20

28 May '20

External Email - Use Caution Hi Bruce, The talairach transform is reasonable and the aseg segment the cc correctly. I run with freesurfer dev version the same command (recon all -autorecon-2wm -subjid post_006) and now I have more information about what could be the problem. The output of the terminal (that you can see below) says that there is a vertex in the curv file of each hemisphere that has one vertex number that it is not expected. When I open the curv file in tksurfer there is a 0 in these positions. Maybe this output can be useful to help me solve the problem. What do you think I should do? Thanks in advance! mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 128 vertices thresholded to be in k1 ~ [-0.27 0.70], k2 ~ [-0.10 0.11] total integrated curvature = 0.637*4pi (8.002) --> 0 handles ICI = 1.5, FI = 8.0, variation=142.940 106 vertices thresholded to be in [-0.03 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 125 vertices thresholded to be in [-0.16 0.23] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.023 done. @#@FSTIME 2020:05:28:10:21:34 mris_curvature N 12 e 52.03 S 0.20 U 51.78 P 99% M 334852 F 0 R 89611 W 0 c 174 w 1 I 0 O 1888 L 2.00 2.00 1.76 @#@FSLOADPOST 2020:05:28:10:22:26 mris_curvature N 12 2.00 2.00 1.77 #----------------------------------------- #@# Curvature Stats lh Thu May 28 10:22:26 CEST 2020 /usr/local/freesurfer/subjects/post_006/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm post_006 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ post_006/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture...error: No such file or directory error: MRISreadNewCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/post_006/surf/lh.curv ***WARNING!*** Some error has occurred while reading 'lh.curv'. This might be due a vertex incompatibility between the surface 'lh.smoothwm' and curv 'lh.curv'. You might be able to correct this by re-running 'mris_make_surfaces' on this dataset. Skipping this (and any remaining) curvature files. Any measurements / calcuations that depend on the curvature file will be skipped. ************* Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 208 ] WARN: S lookup min: -0.238596 WARN: S explicit min: 0.000000 vertex = 1525 @#@FSTIME 2020:05:28:10:22:26 mris_curvature_stats N 11 e 2.95 S 0.14 U 2.79 P 99% M 170736 F 6 R 48708 W 0 c 56 w 7 I 1104 O 7584 L 2.00 2.00 1.77 @#@FSLOADPOST 2020:05:28:10:22:29 mris_curvature_stats N 11 2.00 2.00 1.77 #----------------------------------------- #@# Curvature Stats rh Thu May 28 10:22:29 CEST 2020 /usr/local/freesurfer/subjects/post_006/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm post_006 rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ post_006/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture...error: No such file or directory error: MRISreadNewCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/post_006/surf/rh.curv ***WARNING!*** Some error has occurred while reading 'rh.curv'. This might be due a vertex incompatibility between the surface 'rh.smoothwm' and curv 'rh.curv'. You might be able to correct this by re-running 'mris_make_surfaces' on this dataset. Skipping this (and any remaining) curvature files. Any measurements / calcuations that depend on the curvature file will be skipped. ************* Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 190 ] WARN: S lookup min: -0.040471 WARN: S explicit min: 0.000000 vertex = 53

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fs_install_mcr error
by AmirHussein Abdolalizadeh 28 May '20

28 May '20

External Email - Use Caution Hi all, I have installed FS7 (centOS8 version) on ubuntu 18.04. I try to install MATLAB runtime but it gives an error when I type "fs_install_mcr R2014b": Archive: installer.zip End-of-central-directory signature not found. Either this file is not a zipfile, or it constitutes one disk of a multi-part archive. In the latter case the central directory and zipfile comment will be found on the last disk(s) of this archive. unzip: cannot find zipfile directory in one of installer.zip or installer.zip.zip, and cannot find installer.zip.ZIP, period. Since I suspected it might be an access issue, I have used chmod -R 777 on my FreeSurfer installation category. Also, using "sudo" before "fs_install_mcr" causes the bash not to recognise fs_install_mcr command. Any suggestions? Bests, Amir

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Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)
by Schranzer René 28 May '20

28 May '20

External Email - Use Caution Hi Douglas, First of all, thank you for your help. I forgot to mention that I am already using skull-stripped data for the recon-all processing stream. Therefore, I stopped after -autorecon1 and copied the T1.mgz to brainmask.mgz and brainmask.auto.mgz and continued processing with -autorecon2 and -autorecon3. In some subjects (at some timepoints), the recon-all -autorecon2 -autorecon3 excited with errors, as mentioned below. Now I have used the following command "recon-all -hires -skullstrip -no-wsgcaatlas -s ${sbjID} -i ${sbj} -all" with the skull-stripped data and it worked fine without errors. I also compared the T1.mgz from both approaches and they looked identical. My question, can I use this approach with the "-no-wsgcaatlas" for all subjects or is there something to consider here? Best, René

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lta_convert
by Alshelh, Zeynab 28 May '20

28 May '20

Hi everyone, I am running this version of fs: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 But I am having trouble running lta_convert, it returns with command not found. Is there something I am missing? Thanks ---- Zeynab Alshelh, PhD | Postdoctoral Research Fellow Pain and Neuroinflammation Imaging Laboratory Harvard Medical School | A. A. Martinos Center for Biomedical Imaging Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 Charlestown, MA 02129 +1 (617) 794 6838 zalshelh(a)mgh.harvard.edu | www.nmr.mgh.harvard.edu

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