Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Rendering in 3ds Max?
by Dorian P. 01 May '14

01 May '14

Hi list, Anybody has ever tried to bring Freesurfer pial surfaces for render in 3D studio max? I would be curious on the procedure to follow, more specifically on which file to export/import/convert. Thank you. Dorian TJU

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cortical thickness limit
by Hayyah Clairman 01 May '14

01 May '14

Hello, I have done some comparative cortical thickness analyses in children using FreeSurfer and noticed that the maximum regional thickness value is 5.0. I was wondering if there is an explanation for this limit. Perhaps this is because FreeSurfer was designed for adults? Thank you, Hayyah ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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installing freesurfer on mac
by Demanuele, Charmaine 01 May '14

01 May '14

Hi, I am trying to install freesurfer on my mac, and I got a license key, which I need to save as ".license" file. However, the mac is not allowing me to do so. I tried saving the file in linux and importing to the mac but this failed too. I also tried saving it as freesurfer.license instead of just .license but I get the error: [Charmaines-MacBook-Pro:/Applications/freesurfer] Charm% tkmedit bert orig.mgz Couldn't create output file .xdebug_tkmedit-------------------------------------------------------------------------- ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. Any ideas? Thanks very much, Best, Charmaine --------------------------------------------------------------------------------------- Charmaine Demanuele, Ph.D. Psychiatric Neuroimaging Athinoula A. Martinos Center for Biomedical Imaging Harvard Medical School 149 13th Street Charlestown Navy Yard Charlestown, MA 02129 phone: +1617-724-3170 email: charmd(a)nmr.mgh.harvard.edu <tel:617-726-4078>

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Re: [Freesurfer] Question regarding IGI
by Marie Schaer 30 Apr '14

30 Apr '14

Hi Virendra, Where does this surface come from? You didn't get this one after running the default recon-all, right? Looking at it I noticed a lots of holes and many small unconnected components on the medial aspect. I ran mris_euler_number and got a total of 68 defects, so I'm afraid you'll not be able to run lGI with this surface as the lGI code expect a single continuous surface with no holes. And beside the issue of running lGI until the end, I'm concerned that neither cortical thickness not cortical folding can be reliably estimated based on this surface, and that you'll have trouble registering it to an average template. Best, Marie On Apr 30, 2014, at 3:08 PM, Virendra Mishra <virendra.mishra(a)utsouthwestern.edu<mailto:virendra.mishra@utsouthwestern.edu>> wrote: Hello Marie and other freesurfer users, I am trying to compute IGI for the attached file but at the step of mri_path2label , the code goes into an infinite loop and it is not able to create .label file even for the first .path file. I will be very thankful if you can help me debug this issue. Thank you, Sincerely, Virendra. ________________________________ UT Southwestern Medical Center The future of medicine, today. <lh.pial>

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basic segmentation stats question
by Shantanu Ghosh 30 Apr '14

30 Apr '14

Dear Freesurfers, Pardon me for a very basic question. If I wanted to extract the hemisphere-wise GM and WM values for multiple subjects using a single command, what is the best way to do it? Thanks in advance. Shantanu -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg

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reading ?h.smoothwm.nofix
by Virendra Mishra 30 Apr '14

30 Apr '14

Hello all, Is there a way to read ?h.smoothwm.nofix using freesurfer_fread3() command in matlab? The question that I want to ask really is ?h.smoothwm.nofix should essentially have the same file format as ?h.pial (but I may be wrong) because ?h.*.pial.asc and ?h.*.nofix.asc both have vertices and faces information and I can read ?h.pial using freesurfer_fread3() command. Can anybody help me to read the ?h.smoothwm.nofix file using freesurfer_fread3() command? Thank you for any help. Sincerely, Virendra. ________________________________ UT Southwestern Medical Center The future of medicine, today.

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FS F.5 error
by Elisabetta del Re 30 Apr '14

30 Apr '14

I ran a few cases through freesurfer5.3 last night and > found that they all > exited with the same error. This is the input that I > used: > recon-all -s 01100.t1-realign-masked -i /tmp/01100.t1-realign-masked.nii.gz -autorecon1 && cp /projects/pnl/software/freesurfer5.3b/subjects/01100.t1-realign-masked/mri/T1.mgz /projects/pnl/software/freesurfer5.3b/subjects/01122.t1-realign-masked/mri/brainmask.mgz && recon-all -autorecon2 -subjid 01100.t1-realign-masked && recon-all -autorecon3 -subjid 01100.t1-realign-masked && mv /projects/pnl/software/freesurfer5.3b/subjects/01100.t1-realign-masked 01100.freesurfer > > I've attached the recon-all.log file which shows the > following error: > > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF > ROUTINE MCSRCH ERROR > RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: > FUNCTION OR GRADIENT ARE > INCORRECT OR INCORRECT TOLERANCESoutof > QuasiNewtonEMA: 007: -log(p) = > -0.0 tol 0.000010 > > Thank you so much for any help, best, > > Elisabetta del Re > > -- Elisabetta del Re, instructor, psychiatry, Harvard Medical School

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mri_vol2surf and MNI152_2mm
by JacobML＠nmr.mgh.harvard.edu 30 Apr '14

30 Apr '14

Hello Freesurfer Experts, I was wondering if someone can help me understand which options I need to include with mri_vol2surf for the following situation? I am trying to take group stats generated within FEAT that are in MNI152_2mm space and registrar/project those to fsaverage inflated surface. When I tried a quick visualization using just tksurfer and overlaying my MNI space vol images, there seemed to be anatomical/registration differences between where each space displayed the stats. I then attempted to use mri_vol2surf (command below) in hopes of better aligning these two spaces, but the statistical intensity values have been lost and I am not confident that this command worked in the way I thought it might/would like it to. I am not sure which flags/options may be best in this situation, but any insight you may have is greatly appreciated! Command used: mri_vol2surf --mov /.../tstat2.nii.gz --ref /.../MNI152_T1_2mm_brain.nii.gz --reg fsaverage --mni152reg --hemi rh --surf white --o /.../stats/ Is part of my problem that I have not specified a particular --out_type? Terminal Output: srcvol = /autofs/cluster/ablood/1/jacob/FSL_FEAT_and_MORE/results/groups/BETman_111/12Cv12P_L_tapACT.gfeat/cope1.feat/stats/tstat2.nii.gz srcreg = /usr/local/freesurfer/stable5_3_0/average/mni152.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume WARNING: the voxel resolution in the source volume (2,2,2) differs from that listed in the registration file (1,1,1) Reading surface /space/sake/3/users/inverse/subjects/fsaverage/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 21216 Writing to /autofs/cluster/ablood/1/jacob/FSL_FEAT_and_MORE/results/groups/BETman_111/12Cv12P_L_tapACT.gfeat/cope1.feat/stats/ Dim: 163842 1 1 non-standard value for imnr1 (1, usually 256) in volume structure non-standard value for type (3, usually 0) in volume structure non-standard value for width (163842, usually 256) in volume structure non-standard value for height (1, usually 256) in volume structure Outputed files: COR-001 COR-.info Command used for viewing: tksurfer fsaverage rh white -overlay COR-001 Thank you for the help, Jacob

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MCSRCH
by Elisabetta del Re 30 Apr '14

30 Apr '14

Hi all, I ran a few cases through freesurfer5.3 last night and found that they all exited with the same error. This is the input that I used: recon-all -s 01100.t1-realign-masked -i /tmp/01100.t1-realign-masked.nii.gz -autorecon1 && cp /projects/pnl/software/freesurfer5.3b/subjects/01100.t1-realign-masked/mri/T1.mgz /projects/pnl/software/freesurfer5.3b/subjects/01100.t1-realign-masked/mri/brainmask.mgz && recon-all -autorecon2 -subjid 01100.t1-realign-masked && recon-all -autorecon3 -subjid 01100.t1-realign-masked && mv /projects/pnl/software/freesurfer5.3b/subjects/01100.t1-realign-masked 01100.freesurfer I've attached the recon-all.log file which shows the following error: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) =-0.0 tol 0.000010 Thank you so much for any help, best, Elisabetta del Re -- Elisabetta del Re, instructor, psychiatry, Harvard Medical School -- Elisabetta C. del Re, Ph.D. Instructor, Department of Psychiatry Harvard Medical School phone 617 9675569 mail elisabetta_delre(a)hms.harvard.edu

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Segmentatoin fault using Freesurfer Functions Fedora 19 - Freesurfer 5.1
by West, John D. 30 Apr '14

30 Apr '14

Hello. We are trying to get Freesurfer 5.1 to work on Fedora 19. The functions we have tried show the help menu successfully when asked, but run into a Segmentation Fault when trying to process anything. Both tkmedit and mri_convert have shown this behavior. Segmentation Faults are notoriously hard to track down, but do you have any suggestions as to what may be causing this? This version of freesurfer seems to work fine on fedora 17 and older. We are using the CentOS4 x86_64 version of Freesurfer 5.1. Thanks. -John West Systems Administrator IU Center for Neuroimaging

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