Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30087 discussions

Segmentation Issues
by Harriet Cornwell 24 Mar '20

24 Mar '20

External Email - Use Caution Hello, We are using FreeSurfer v5.3. and are sometimes finding that a brain can seem okay when it is first run through the recon-all process and is edited, but then when it is re-run the segmentation seems to deteriorate hugely. I have screenshotted an example below. Are you able to advise us on why this might be happening and what we could do about this? One of the options I had thought about was to re-run the recon-all from scratch but it doesn’t seem very time efficient to do this for multiple brains. Any suggestions would be gratefully received! Thank you.

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SurfaceRAS and RAS coordinates are different on reconstructed surface of monkey
by wangzhiwei3233 23 Mar '20

23 Mar '20

External Email - Use Caution Hello FreeSurfer Developers, I am trying to reconstructing surface of monkey brain. I have got surface files, such as ?h.white, ?h.pial, ?h.area and so on. However, I found the surface light was abnormally dark(as shown in following picture), it seems like that the light source was inside the brain. And I found the RAS and SurfaceRAS coordiantes were different. I got the surface files as following steps: (1) I got the wm.mgz file manually; (2) I filled the wm.mgz and changed the values in left and right hemispheres to 255 and 127, respectively; (3) I generated ?h.orig via command "mri_tessellate filled.mgz 255 lh.orig -n" Then I found RAS and SurfaceRAS coordiantes in ?h.orig were different. Which steps did I made a mistake? The voxel size of raw image was 0.5*0.5*0.5 mm, was the image resolution the cause? Thank you very much! zhiwei here is the information of raw image: Volume information for T1.mgz type: MGH dimensions: 137 x 175 x 107 voxel sizes: 0.500000, 0.500000, 0.500000 type: FLOAT (3) fov: 87.500 dof: 0 xstart: -34.2, xend: 34.2 ystart: -43.8, yend: 43.8 zstart: -26.8, zend: 26.8 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -6.0000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 3.7500 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 0.5000 0.0000 0.0000 -33.7500 0.0000 0.5000 0.0000 -49.7500 0.0000 0.0000 0.5000 -23.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 0.125 ras to voxel transform: 2.0000 0.0000 0.0000 67.5000 0.0000 2.0000 0.0000 99.5000 0.0000 0.0000 2.0000 46.0000 0.0000 0.0000 0.0000 1.0000

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R-version of read_annotation.m
by Athanasia Monika Mowinckel 23 Mar '20

23 Mar '20

External Email - Use Caution Hi. I’m closing in on a version of read_annotation.m that runs entirely in R. I know I am not the only one wanting something not needing Matlab, and my initial idea was to contribute this version (acknowledging Bruce in the documentation as the author of the original function of course), to the Freesurfer R package (https://github.com/muschellij2/freesurfer) I wanted to check in with you first on how and if this was ok, or if you have other suggestions to how this can be shared. All the best, Athanasia Monika Mowinckel Staff scientist Phone: +47 22845022 e-mail: a.m.mowinckel(a)psykologi.uio.no<mailto:a.m.mowinckel@psykologi.uio.no> Center for Lifespan Changes in Brain and Cognition (LCBC) Department of Psychology University of Oslo POB 1094 Blindern 0317 Oslo Norway [LCBC] <https://www.oslobrains.no/> [Lifebrain] <https://www.lifebrain.uio.no//>

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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

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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

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