Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

how to make label from volumetric mask?
by Niia Nikolova 15 Dec '16

15 Dec '16

Dear Freesurfers, I have some binary ROI masks of MT/V5 that I’ve drawn from activation maps in fslview, which I would like to transform into labels so that I can project them onto a surface and flat patch. I have been following parts of this thread https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32468.html <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32468.html> and have tried using mri_vol2surf and mri_cor2label, but I cannot view the result either with tksurfer or freeview. I would like to be able to load the subjects inflated surface with tksurfer, and add the mask as a label, or something similar. The commands I’ve used are as follows: mri_vol2surf —src MST_L_bin.nii.gz —out MST_L_surf.mgh —out_type mgh —hemi lh —srcreg MST_L_to_BGimage.dat —projdist 0.5 —ref MST_L_bin.nii.gz mri_cor2label —i MST_L_surf.mgh --id 1 —l lh.mst.label I previously created MST_L_to_BGimage using fslregister. I am also attaching the input mask file as well as the label file that I generated in this way. Are these the right programs to use in this case, and if so, what is the appropriate way of using them? Thank you in advance for any help. Sincerely, Niia

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problem of using freesurfer
by Hsin-Tsung Lee 15 Dec '16

15 Dec '16

Dear freesurfer community I have used the freesurfer v5.30 stable on linux, I want to fusion the CT image and the MRI T1 image. The CT image was signed form the epilepsy patient after the inserted depth electrode surgery. The MR image was sign before the operation. I tried to register them by the "bbregister" or "mri_robust_register" , but it didn't work good. And I had seen the website page " https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-June/046081.html" , does the "mri_coreg" is the better instruction to use in my case? And, I found that I can't find the download link of freesurfer v6.0 in your website, and the link " ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg.mac " is invalid to use. I really appreciate any help here HsinTsung Lee

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incorrect pial surfaces after watershed adjustment
by Rizvi, Batool 15 Dec '16

15 Dec '16

Hi FreeSurfer experts, We have a subject on which we had to do adjust the watershed parameters for, since there was some brain missing from the brainmask.mgz. The watershed itself worked, but after that, we needed to regenerate the surfaces after the bad skull strip was fixed, and we ran "recon-all -autorecon-pial -subjid <subject name>" That seemed to not work though, and it still shows that the surfaces do not include the new brain matter. Attached is an image of the output. Is there anything else we can try to regenerate these surfaces correctly? Thank you! Batool

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"Can't locate shellwords.pl" error
by Aquino Domenico 15 Dec '16

15 Dec '16

Dear Freesurfer team,, I'm trying to segment a pre-processed 3D PSIR volume. After few minutes Freesurfer return the following error: mritotal -verbose -debug -clobber -modeldir /Applications/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.12174/src.mnc transforms/talairach.auto.xfm Can't locate shellwords.pl in @INC (@INC contains: /Applications/freesurfer/mni/bin/../lib/mni_autoreg /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.10.0/darwin-thread-multi-2level /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.10.0 /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at /Applications/freesurfer/mni/bin/mritotal line 460. ERROR: mritotal failed, see transforms/talairach.log I can't understand which could be the problem. In attachment you'll find the log file. Could you please help me? Thanks a lot, Domenico ___________________________________________ Eng. Domenico Aquino Department of Neuroradiology IRCCS Foundation Neurological Institute "Carlo Besta" Via Celoria,11-20133 Milano Phone: +39 02 23942472 Fax +39 02 23942543 [1463859753944_LogoWhite.jpg]

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recon-all <subjid> -localGI
by André Schmidt 15 Dec '16

15 Dec '16

Dear FS experts I am trying to run the recon-all <subjid> -localGI command, but unfortunately I receive the following error message (see attached the log file): Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); EDU>> ERROR: make_roi_paths did not complete successfully! Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64 recon-all -s HC001 exited with ERRORS at Thu Dec 15 07:49:18 GMT 2016 I would be very grateful if you could let me know what went wrong here? All subjects were pre-processed using the recon-all all command so all required files should be available. Thank you very much for your help. Best wishes André

1 0

Using different atlas in aparcstats2table command
by Martin Juneja 14 Dec '16

14 Dec '16

Hi, I would like to use aparcstats2table command. By default, it uses Killiany/Desikan parcellation atlas. But I would like to use atlas by Yeo and colleagues ( https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011) Could you please let me know how can I use this atlas instead of default --parc and what would be the aparcstats2table command for this? Thanks.

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Content of PET gtm.stats.dat file
by Donatas Sederevicius 14 Dec '16

14 Dec '16

Hello FreeSurfer Developers, I have run mri_gtmpvc command to perform PET PVC (partial volume correction) where input data has 4 frames (dynamic). The output volume as gtm.nii.gz has 4 frames as well which means that PVC was performed for each frame separately. However, gtm.stats.dat file has one value for each ROI. At first I thought it was the average of all frames but after manually comparing some ROIs it seems that the values in the file are taken only from the first frame of dynamic data. Is it the case or those values have another interpretation? Maybe it is the highest value across all frames? In addition, is there an easy way to get the same file where the values would be the average across all frames?

2 1

-FLAIRpial; T2 SPACE
by Octavian Lie 14 Dec '16

14 Dec '16

Dear All, Our MPRAGE and T2 SPACE FLAIR sequences are acquired at times during two different scans, and the MPRAGE seq further gets reoriented in a pipeline upstream of the Freesurfer step. For best results, does the FLAIR volume have to be reoriented (and resliced) in a rigid registration to the MPRAGE before recon-all -all stage, or it does not matter? Thank you, Octavian

2 1

Label creation
by Leyton Moscoso, Cristian Eduardo 14 Dec '16

14 Dec '16

Hi Freesurfer's experts Is there an easy way to create automatically a circular label with a radius centered on a vertex with predifined RAS/Tailarach coordinates on the fsaverage surface? Thanks Cris

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5.3v migration
by Eduard Vilaplana Martinez 14 Dec '16

14 Dec '16

Dear FS experts, We are planning to update all our subjects from de 5.1v to 5.3v. Our subject database processed with the 5.1v is really big so we are thinking about ways to not start over new. Is there any way to take advantage of the 5.1v segmentations? We have been thinking about using a dilated version of the already corrected 5.1v aparc+aseg as a brainmask for the new segmentation. Any ideas would be appreciated. Is there any standarized way to carry out this kind of process? And is there any way to take profit from the wm segmentation of the older version? Thanks in advance, Edu V.

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