Freesurfer December 2016

freesurfer@nmr.mgh.harvard.edu

95 participants
146 discussions

questions about registration tool in Freesurfer
by Frank Robert 15 Dec '16

15 Dec '16

Dear FS experts I want to use Freesurfer registration tools. I check https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommandsRegistration?hi… 1). Here it is the term " modality" I want to get clarification. It is easy to know Modality is different between CT, MRI and PET. But if MRI use different sequence, T1, T2, DWI, ASL to get different images, it is the same modality or different modality? 2). mri_coreg is strongly recommended for use. But I can not find the instruction in Wiki. 3.) If I register ASL source image and subtraction images to T1w images, I guess that preciseness of registration will be higher if use source images to register. Is it right? If it is correct, If I use ASL source images to register to get .lta file, how can I apply .lta file to apply for subtraction images? Do you have instruction? Many thanks Best Regards Frank Yu

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(no subject)
by Sadhana Singh 15 Dec '16

15 Dec '16

Hi I am using freesurfer for calculation cortical thickness in my subjects. Firstly, I have converted all the T1 weighted images from dcm into nii.gz format. After that, I have run the recon-all in one subject using this script 'recon-all -i CON_101.nii -s CON_101 -all' , but it shows error The error is: [kumarlab@lcmodel ~]$ cd /home/kumarlab/Downloads/ Freesurfer_VBM [kumarlab@lcmodel Freesurfer_VBM]$ export SUBJECTS_DIR=/home/kumarlab/ Downloads/Freesurfer_VBM [kumarlab@lcmodel Freesurfer_VBM]$ recon-all -i CON_101.nii -s CON_101 -all ERROR: cannot find CON_101.nii Linux lcmodel 3.10.0-327.el7.x86_64 #1 SMP Thu Oct 29 17:29:29 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Thu Dec 15 16:14:29 EST 2016 Regards *Sadhana Singh, PhD *

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mri_coreg question
by Frank Robert 15 Dec '16

15 Dec '16

Hello FS experts I followed the instruction to download the mri_coreg file from website https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_coreg put it on my virtual machine ubuntu \local\user\freesurfer\bin directory. But I run it and it say <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_coreg> \local\user\freesurfer\bin\mri_coreg can not execute binary file? I use sudo chmod u+x mri_coreg to make it executable. Do you know why? Frank Yu Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Oct 3 to freesurfer you can get it from here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_coreg On 10/03/2016 12:46 PM, Hsin-Tsung Lee wrote: > Dear Dr. Bruce > I have one more question, does the "mri_coreg" available in > version 5.30 stable, or it only available in v6.0(or it's beta version)? > > Best Regard

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Infant brain atlas
by Axelson, Eric D 15 Dec '16

15 Dec '16

I asked this last week with no response: Does the infant brain atlas mentioned in this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/ exist yet or will it be included in version 6? Thanks Eric Axelson Research Specialist Department of Psychiatry University of Iowa eric-axelson(a)uiowa.edu<mailto:eric-axelson@uiowa.edu> ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

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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

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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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Freesurfer December 2016