Freesurfer October 2019

freesurfer@nmr.mgh.harvard.edu

111 participants
180 discussions

FW: Mapping coordinates from sphere file to ?h.white
by Glasser, Matthew 28 Oct '19

28 Oct '19

External Email - Use Caution From: Timothy Coalson <tsc5yc(a)mst.edu> Reply-To: Timothy Coalson <tsc5yc(a)mst.edu> Date: Monday, October 28, 2019 at 8:21 PM To: "Glasser, Matthew" <glasserm(a)wustl.edu> Subject: Re: FW: [Freesurfer] Mapping coordinates from sphere file to ?h.white That is not a sphere of fs_LR coordinates (in fact, "fs_LR coordinates" is not really a meaningful phrase). That sphere's per-vertex coordinates are specifically intended to spatially line up our fs_LR atlas data to fsaverage atlas data on the fsaverage atlas sphere, because this is the information needed to resample between the atlases. It has the same number of vertices as fs_LR surfaces because it needs to know the target location on the fsaverage atlas sphere for every fs_LR vertex. The inflation of an anatomical surface to a sphere is a tricky process, as the surface can easily fold back over itself (which would encode a non-invertible transformation). The path the vertices took to get to a sphere is neither recorded, nor particularly important to anyone not working on the implementation details of the inflation. The endpoint of the process, the spherical surface, is the only goal, the displacement vectors between them are not useful to surface operations (since the data is tied to the vertices, and all the vertices still exist in the sphere (just at new coordinates), it is trivial to use the same data "on" either the sphere or anatomical surfaces). These spherical surfaces are only used to do registration and resampling (which does not involve any kind of warp of anatomical coordinates), after which the data is used with anatomical surfaces (which always maintain the original shape and size even when resampled), because spatial processing should be done on brain-shaped geometry, not on spheres. It is unclear to me what you intend to use the surface you described for, and I don't know what the .x5 format is. The surface resampling weights are fairly easily derived from the correct pair of spheres, and resampling does not involve any kind of spatial displacement. Tim From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Oscar Esteban <phd(a)oscaresteban.es<mailto:phd@oscaresteban.es>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, October 28, 2019 at 6:58 PM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Mapping coordinates from sphere file to ?h.white External Email - Use Caution Dear experts, In the context of the BIDS transforms extension and the ".x5" format we chatted about in the workshop we made in March at MIT, we are addressing the following question. We have a sphere of fsLR coordinates in fsaverage space (e.g., https://github.com/Washington-University/HCPpipelines/blob/master/global/te… - but the question extends to the right hemisphere and also resolutions other than 59k). We want to expand this sphere to the fsaverage's white surface (lh.white, in this example). Since coordinates on the fsLR sphere don't match any of fsaverage{,3,4,5,6}'s coordinates, we wonder whether FreeSurfer stores somewhere/somehow the analytical transform of this mapping. In other words, how one would map arbitrary coordinates on the surface to a particular fsaverage's white (or midthickness, or pial, etc.) surface. Otherwise, I guess I would pick fsaverage's surfaces (i.e., 7th degree icosahedron), and interpolate the displacement vectors that start at each sample on the surface and end at the corresponding location of that vertex index of the destination surface (lh.white for the example above). Is there any tool that actually does the _inverse transform of the surface-to-sphere mapping_? Thanks very much. Regards, Oscar -- ___________________________ Oscar Esteban, Ph.D. Postdoctoral Fellow, Poldrack Lab Stanford University +1 (650) 733 33 82 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] username and password
by fsbuild 28 Oct '19

28 Oct '19

External Email - Use Caution OK, thanks for letting us know.   We will look into when/how that redirect started to happen.  Just to clarify though, you do not need to login to the Martinos center to download the freesurfer release binaries or source code, i.e., using that form was just to get on the freesurfer mail list. The Freesurfer 6.0  release binaries (for Linux and MacOS) can be downloaded from, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall The latest development branch with the freesurfer source code can be obtained from GitHub, https://github.com/freesurfer/freesurfer - R. Rachel S October 2, 2019 at 15:36         External Email - Use Caution        Hi, I have the same problem. It directs me to the Martinos Centre Login, which never happened before. I've subscribed to the maillist. Best,Rachel _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer fsbuild October 1, 2019 at 16:08         External Email - Use Caution        Hello Takashi, Did you create a login to the list on this page, http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - and then receive the email notification, and then did you do the confirmation step? - R. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_cvs_register error while diffusion imaging processing
by Renew Andrade 28 Oct '19

28 Oct '19

External Email - Use Caution Dear FreeSurfer experts: I am trying to run Spatial Normalization but I cannot get the morph file because I get this error. I don’t know what to do with these libraries. Do I need to copy them from where they are in freesurfer to somewhere else in the Mac? sh-3.2# mri_cvs_register --mov IXI_25_Guys_T1 Using the CVS template as registration target... The outdir: /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/cvs Log file is /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/cvs/IXI_25_Guys_T1_to_cvs_avg35.mri_cvs_register.1910241722.log Thu Oct 24 17:22:55 CEST 2019 --mov IXI_25_Guys_T1 $Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $ Renes-Air.home Darwin Renes-Air.home 19.0.0 Darwin Kernel Version 19.0.0: Wed Sep 25 20:18:50 PDT 2019; root:xnu-6153.11.26~2/RELEASE_X86_64 x86_64 asegfname aseg Using m3z type morph files. dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Abort Sincerely, Andrade.

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recon-all at native resolution
by Alexopoulos, Dimitrios 28 Oct '19

28 Oct '19

External Email - Use Caution We have data acquired at 0.8mm isotropic and would like to maintain this resolution in the processing stream rather than FS resampling to 1mm. Is the command to do this 'recon-all -hires -all'? Are there any drawback to doing this? Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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view labels in native space
by Nasiriavanaki, Zahra 28 Oct '19

28 Oct '19

Hi Freesurfer experts I have a few labels that correspond to activation clusters in fsaverage space for an individual subject. I used mri_label2label to transfer them to native space of the subject. export SUBJECTS_DIR=/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR mri_label2label --srclabel ./first_levels/$subj/label/aparc/pos/lh-0001.label --trglabel lh-new.label --srcsubject fsaverage --trgsubject ${subj} --regmethod surface --hemi lh When I overlay the native label on top of the fsaverage significance map (tksurfer fsaverage lh inflated -ov sig.nii.gz), it looks like small dots all over the map. Is this because I'm viewing the native label in fsaverage space? Is there a way to view these labels in this subject's native space instead of fsaverage, something like tksurfer native(instead of fsaverage) lh inflated -ov sig.nii.gz? Thank you very much in advance Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Re: [Freesurfer] Error in glmfit-sim cache
by Renew Andrade 28 Oct '19

28 Oct '19

External Email - Use Caution I don’t know what do you mean by not knowing what it means. I said that I have tried all the values the error pinpoints to. That is I have tried mri_glmfit-sim --glmdir lh.IXI.glmdir --cache 4 abs —cap 0.05 --2spaces with "1.3", "2.0", "3.0", “4.0”. And it doesn’t work. I know it doesn’t seem to be a software issue but I cannot run this functionality of the software only for the moment everything else works fine. I have two laptops one Mac and one BMAX I have done recon-all in one and I have done glmfit in the MAC. But this I hope is only temporary because makes no sense that a software works partially. Sincerely, Andrade. ERROR: > thresh = 4,0 must be 1.3, 2.0, 3.0, 4.0 I don't know what this refers to On 10/18/19 4:45 PM, Renew Andrade wrote: > External Email - Use Caution > > I have tried all the values it pinpoints to but none seem to work. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

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Vertex and voxel-wise linear regression in Freesurfer
by Larry Lai 28 Oct '19

28 Oct '19

External Email - Use Caution Hello FreeSurfer Users I'm attempting to explore the correlations between the surface-based and voxel-based values and adjusted for nuisance covariate in FreeSurfer. *Correlational study:* A. Cortical thickness and VBM results B. VBM_1 and VBM_2 results *Platform:* 1) freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Ubuntu 16.0.4 Thanks for considering my request. Best regards -- *Ying-Liang (**Larry)** Lai, Ph.D. Student* Research Assistant *Ph.D. Program for Neural Regenerative Medicine* College of Medical Science and Technology Taipei Medical University and National Health Research Institutes

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b0 to T1’s co-registration without b0 inhommogeneities
by Daniel Callow 28 Oct '19

28 Oct '19

External Email - Use Caution Hello, I am trying to do a within-subject co-registration between b0 volumes and T1's for my subjects. This is an old dataset that does not have anything for correcting b0 inhomogeneities. The registration using --dti and normal parameters for bbregister led to "okay" within-subject registration. I am wondering if modifying the --dof (like 12) option for bbregister or applying some type of linear/nonlinear registration might improve the registration? 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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Could you help me to extract my brain from MRI?
by satyr96＠o2.pl 27 Oct '19

27 Oct '19

External Email - Use Caution Hello. I have spent a lot of time testing different options in freesurfer to extract my brain for 3D printing but I could not get good results (like different parameters for skul removal and multiple images). I think the issue is with my image is to crappy because when I have used perfect MRI scan (now I think it could have been human sliced after dead) the brain looks perfect and I was able to 3D print it. I attachment I am sending the comparation between results. Link to my MRI images and final STL files: drive.google.com drive.google.com Please remove any private info if I left any. Please help me to create my own 3D model of brain. Best regards, Adam

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ERROR: Must specify input table of gradient vectors
by Renew Andrade 26 Oct '19

26 Oct '19

External Email - Use Caution Dear Anastasia Yendiki: I have tried to run TRACULA on 3 subjects as specified in configuration file attached. But the terminal output is: sh-3.2# trac-all -prep -c dmrirc.IXI domainname: Command not found. Too many ('s. INFO: SUBJECTS_DIR is /Volumes/FREESURFER/freesurfer_preprocessed INFO: Diffusion root is /Volumes/FREESURFER/freesurfer_preprocessed Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/dmrirc.local -log /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/trac-all.log -cmd /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Sat Oct 26 23:06:34 CEST 2019 mri_convert --bvec-voxel /Volumes/FREESURFER/old_databases/copy_IXI/IXI025-Guys-0852-T1.nii.gz /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /Volumes/FREESURFER/old_databases/copy_IXI/IXI025-Guys-0852-T1.nii.gz /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/FREESURFER/old_databases/copy_IXI/IXI025-Guys-0852-T1.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0506412, -0.996042, 0.0730476) j_ras = (0.00618997, 0.073453, 0.997279) k_ras = (0.998698, 0.0500512, -0.00988522) writing to /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz... ERROR: Must specify input table of gradient vectors Darwin Renes-Air.home 19.0.0 Darwin Kernel Version 19.0.0: Wed Sep 25 20:18:50 PDT 2019; root:xnu-6153.11.26~2/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Sat Oct 26 23:06:39 CEST 2019 I don’t understand why? Because I think I have specified everything correctly. May be there is an issue with “bvecs” and “bvals” files because I added .txt format manually for it to be equal to what is specified in the tutorial of TRACULA configuration file. Sincerely, Andrade.

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Freesurfer October 2019