Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Re: [Freesurfer] format bvalues bvectors tracula
by Renew Andrade 22 Mar '20

22 Mar '20

External Email - Use Caution Dear Yendiki Anastasia: I am replying for second time. I haven’t received an answer about this issue. I don’t know if it is silly but I don’t know how to fix it. It is not / slashes in this case. Sincerely, Andrade.

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Surface meshes of hippocampal subfields
by Casey Paquola 22 Mar '20

22 Mar '20

External Email - Use Caution Dear Freesurfer experts. Is it possible to retrieve the mesh representations of the hippocampal subfields using the latest 7.0 development version of segmentHA_T1.sh? I noticed that the meshes are saved as .txt files in the tmp directiory (following https://surfer .nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala). Is it possible to keep these output files? Also, what format are meshes in within the txt file? Many thanks, Casey

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Re: [Freesurfer] SPM Volumes on FSAVERAGE surfaces
by Ryne Nichols 21 Mar '20

21 Mar '20

External Email - Use Caution I could do that, but for consistency with the some other results, it would be nice if I could get them on FSAVERAGE instead. Are there any good ways to do that other than registering an MNI brain to the fsaverage T1 and carrying the statistical image with it? thanks! > > Message: 16 > Date: Fri, 20 Mar 2020 10:47:41 -0400 > From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] SPM Volumes on FSAVERAGE surfaces > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <10178766-753c-672f-3621-725f033f5a16(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Try running recon-all on the mni152 > > On 3/18/2020 5:05 PM, Ryne Nichols wrote: > > > > ????????External Email - Use Caution > > > > All, > > > > I'm having trouble getting good surface projections of SPM results. My > > SPM results come from SPM normalization -- which should be MNI152 space. > > > > I'm confused because fsaverage says it is in MNI305 space. > > > > I've tried a few commands, but the two that confuses me the most is: > > > > mri_vol2surf --mov SPMT_001.nii --mni152reg --trgsubject fsaverage > > --hemi lh --out lh_spm.mgh --projfrac-max 0 1 .1 > > > > Also the similar command: > > > > mri_vol2surf --mov SPMT_001.nii --reg > > $FREESURFER_HOME/average/mni152.register.dat --trgsubject fsaverage > > --hemi lh --out lh_spm.mgh --projfrac-max 0 1 .1 > > > > both give results in a wildly different place on the brain than they > > should be -- it flips the SPMT_001.nii in the Y direction. > > > > If I do > > > > mri_vol2surf --mov SPMT_001.nii --regheader fsaverage --hemi lh --out > > lh_spm.mgh --projfrac-max 0 1 .1 > > > > things are close, but nor exactly how they should be (it seems). > > > > Finally, if i use a surface that's in MNI152 space > > (cvs_avg35_inMNI152) things look the way they should, e.g.: > > > > mri_vol2surf --mov SPMT_001.nii --regheader cvs_avg35_inMNI152 --hemi > > lh --out lh_spm.mgh --projfrac-max 0 1 .1 > > > > thank you for any help you may provide! > > > > -ryne > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Error with recon-all: You are trying to re-run an existing subject with (possibly) new input data (-i).
by Peng Liu 21 Mar '20

21 Mar '20

External Email - Use Caution Dear all, I am trying to run recon-all command for a subject ben. Before I perform this command, I have exported SUBJECTS_DIR to a folder with only T1 data for this subject ben in it. However after I entered the command "recon-all -s ben -i T1.nii -all", this error showed up: ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags. I have tried all the suggestions listed in the error information, but none worked. Does anyone have any suggestion? I would really appreciated it. Many Thanks Peng -------------------------------------------- Peng Liu, PhD Candidate Institut für Kognitive Neurologie und Demenzforschung (IKND) Otto-von-Guericke Universität Magdeburg Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) Leipziger Str. 44| Haus 64| Raum 217 39120 Magdeburg, Deutschland Email: peng.liu@med.ovgu.de/Peng.Liu@dzne.de Phone: +49 391 67 25074

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Issue with MATLAB 2012 runtime download
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 20 Mar '20

20 Mar '20

External Email - Use Caution Dear Freesurfer experts, I'm having an issue while attempting to download Matlab 2012 runtime for its use in the hippocampal subfield segmentation. The error is: "Warning: Failed to create the file runtime.tar.gz: Permission denied". See details below: curl " https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&d…" -o "runtime.tar.gz" % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0Warning: Failed to create the file runtime.tar.gz: Permission denied 0 656M 0 7771 0 0 15040 0 12:43:08 --:--:-- 12:43:08 15060 curl: (23) Failed writing body (0 != 7771) Any ideas why this is happening? Thank you, Alex

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extracting values of each voxel within an ROI
by Nasiriavanaki, Zahra 20 Mar '20

20 Mar '20

Hi all Is there any command for extracting the fmri activation from all voxels in an ROI? I know I can use funcroi-config, funcroi-sess and funcroi-table-sess to extract the average activation in a specific ROI from a specific contrast. But what if I want to extract the values of each voxel within that ROI? I appreciate any comments on this. Thanks Mona

2 2

Skull-stripped brain for non-T1 image
by Xiaojiang Yang 20 Mar '20

20 Mar '20

External Email - Use Caution Hi everyone, Suppose I have run Freesurfer with respect to a subject using the T1 image, and I have gotten the skull-stripped brain image (brain.mgz) in the <subjectid>/mir directory. Now I have a non-T1 image of the same subject, say, the (T2)FLAIR series, and I want to get the corresponding skull-stripped brain image of that FLAIR series by using some kind of registration. How should I do that? Please advise. Thank you! Xiaojiang

2 1

Flip left-right orientation command
by Miguel Ángel Rivas Fernández 20 Mar '20

20 Mar '20

External Email - Use Caution Dear Freesurfer experts, Which command should I use to flip the left-right orientation of a T1 image?. Actually my image is in PIR orientation, I used the following command mri_info --orientation '/home/rmn/Desktop/study/E03/3d/coanat_E03.nii' *PIR* Thanks in advance, Best regards, -- *Miguel Ángel Rivas Fernández*

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SPM Volumes on FSAVERAGE surfaces
by Ryne Nichols 20 Mar '20

20 Mar '20

External Email - Use Caution All, I'm having trouble getting good surface projections of SPM results. My SPM results come from SPM normalization -- which should be MNI152 space. I'm confused because fsaverage says it is in MNI305 space. I've tried a few commands, but the two that confuses me the most is: mri_vol2surf --mov SPMT_001.nii --mni152reg --trgsubject fsaverage --hemi lh --out lh_spm.mgh --projfrac-max 0 1 .1 Also the similar command: mri_vol2surf --mov SPMT_001.nii --reg $FREESURFER_HOME/average/mni152.register.dat --trgsubject fsaverage --hemi lh --out lh_spm.mgh --projfrac-max 0 1 .1 both give results in a wildly different place on the brain than they should be -- it flips the SPMT_001.nii in the Y direction. If I do mri_vol2surf --mov SPMT_001.nii --regheader fsaverage --hemi lh --out lh_spm.mgh --projfrac-max 0 1 .1 things are close, but nor exactly how they should be (it seems). Finally, if i use a surface that's in MNI152 space (cvs_avg35_inMNI152) things look the way they should, e.g.: mri_vol2surf --mov SPMT_001.nii --regheader cvs_avg35_inMNI152 --hemi lh --out lh_spm.mgh --projfrac-max 0 1 .1 thank you for any help you may provide! -ryne

2 1

Failed to load Surface lh.white
by Alexander Barnett 20 Mar '20

20 Mar '20

External Email - Use Caution Hello FreeSurfer Developers, I am trying to inspect the white matter gray matter surface to verify its accuracy as described in (http://freesurfer.net/fswiki/FsTutorial/ControlPointsV6.0) When I try to open freeview freeview -v 101/mri/brainmask.mgz \ -f 101/surf/lh.white:edgecolor=yellow I get an error that says it Failed to load Surface 101/surf/lh.white. The brainmask.mgz opens fine. When I looked in the /101/surf/ folder, I see lh.white.H, lh.white.K, lh.white.preaparc, lh.smoothwm, but there is no lh.white file. When I inspect the ReconAll table (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) I see that there is no step that creates ?h.white files in V6.0 (note: there is a step that will make lh.white in V5.3). How can I properly assess the white matter gray matter surface in V6.0? 1) FreeSurfer Version: freesurfer-i386-apple-darwin11.4.2-stable6-20170119 2) Operating system : MacOS High Sierra version 10.13.6 3) recon-all.log: see attached ReconAllTableStableV6.0 - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0> This table shows the recon-all steps for the stable, publicly released, version 6.0 of FreeSurfer (available here).. See also the OtherUsefulFlags for other recon-all options. surfer.nmr.mgh.harvard.edu Alex Barnett, PhD Postdoctoral Scholar UC Davis, Center for Neuroscience Dynamic Memory Lab

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