Freesurfer

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30086 discussions

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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re finding sulcal folding values
by Anna Jonsson 30 Apr '14

30 Apr '14

Hi I would like get a mean sulcal folding value per hemisphere and roi data. I have two questions: Is possible do sulcal depth analysis using qdec? And What is the exact command to pass to mris_anatomical_stats to get a mean sulcal depth value /per hemisphere? I have tried some few variations with no luck. Thank you for your help, Kind Wishes, Anna

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repost: mri_convert Siemens Skyra .IMA CentOS5.7 FS5.3
by prasser 29 Apr '14

29 Apr '14

Hi, I am still having some concerns using mri_convert on Skyra volumes that I'm hoping can please be addressed. On this occasion I have used mri_convert to convert a single dicom file to nifti from a volume collected on a siemens Skyra scanner using Freesurfer5.3 on CentOS5.7. When viewing this nifti image using tkmedit it appears 'cut-up' over many sagittal slices (please see attached) rather than the whole image appearing on one plane. Not sure if this is an issue with tkmedit or mri_convert? This problem persists if i convert the entire volume, with this 'cutting' appearing as vertical lines in the image. This is also the case when using the new mri_convert patch for OS X. Lastly, I can upload a dicom file if needed. Thanks, Paul

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p values for within-subject t maps
by JacobML＠nmr.mgh.harvard.edu 29 Apr '14

29 Apr '14

---------- Forwarded message ---------- Hello Doug et al., I was wondering if anyone could give me some information about whether a p value can be associated with t maps generated in individual subjects (across one or two runs) for fMRI data. When doing group contrasts an uncorrected p value can be assigned based on the number of subjects (using that to determine degrees of freedom). However, what are the degrees of freedom for within subject analyses? Does it relate to number of TRs at all? The question stems from wishing to state the uncorrected p value associated with t thresholds from these maps that we used to extract BOLD timecourses. Thank you! Anne ------------------------------- Anne J. Blood, Ph.D. Director, Mood and Motor Control Laboratory Departments of Psychiatry and Neurology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital CNY 149-2301, 13th St. Charlestown, MA 02129 phone: (617) 643-2297 fax: (617) 726-7422 email: ablood(a)nmr.mgh.harvard.edu

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