Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

freesurfer design
by Dijkshoorn, A.B.C. (Aicha) 04 Dec '17

04 Dec '17

Dear freesurfer group, I have two questions: Can I compare one patient with a created control group in Freesurfer on the following outcome measures: cortical thickness, brain volume and gyrification? If so, how can you visualise that? When you do the cortical analysis with freesurfer can you account for covariates in the statistical model (before visualisation)? Kind regards, Aicha Dijkshoorn

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Clarification about "Per-Run" Motion Correction and Registration in Preproc-Sess
by Taylor, Johnmark 04 Dec '17

04 Dec '17

Hello, A few quick questions about the "Per-Run" option in preproc-sess. I understand that in this option, each run's images are registered to the middle timepoint of that run, rather than the first timepoint of the first run. I was wondering, though: 1) Why is this the preferred option instead of per-session? 2) If motion-correction is only done internally to each run, then wouldn't between-run motion throw things off if you wanted to do a GLM spanning the whole scanning session (although I assume it'd be fine for single-run GLMs)? What ensures that the images line up properly between runs? Thank you very much, JohnMark

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mri_binarize
by John Anderson 04 Dec '17

04 Dec '17

Dear FS experts, I want to use mri_binarize to create (binarized and free of CSF and ventricles) mask from "aparc.DKTatlas+aseg". How can I substract CSF and ventricles from teh atlas using mri_binarize? Thanks John

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MRI protocol for hippocampal subfield segmentation
by Gabor Perlaki 04 Dec '17

04 Dec '17

I've two questions regarding hippocampal subfield segmentation: 1, Is there any article or other document which containes an optimal T2 protocol with detailed sequence parameters for hippocampal subfield segmentation? (eg. BW, echo time, repetition time, FOV, echo train, paralell imaging on/off, ...) We have a Siemens Prisma 3T scanner. 2, For T1, we use the suggested MPRAGE protocol by Andre (1mm*1mm*1mm). Is it OK or do we need a special protocol? Thank you, Gabor

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subtract CSF
by John Anderson 04 Dec '17

04 Dec '17

Dear FS experts, I want to create mask from the atlas "aparc.DKTatlas+aseg.mgz". I need the mask to be free of any CSF or ventricles components. Is there any way to subtract these labels (CSF and ventricles) from the atlas "aparc.DKTatlas+aseg.mgz". Thank you for your help John

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Create surface label from MNI152 Coordinate.
by Bastian Cheng 04 Dec '17

04 Dec '17

Dear Freesurfer Experts. Is there a way to create a freesurfer surface label from entering a MNI152 coordinate? I am aware that I can use tcl with tksurfer: mar_vertex X 1 labl_new_from_marked_vertices labl_dilate However as far as I know I can only input vertex numbers, not coordinates. Any helpt would be greatly appreciated! Bastian

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create frontal lobe label
by Vetterman, Richard 01 Dec '17

01 Dec '17

Dear freesurfer group, I tried to create a frontal lobe label but it gives the following error message. Do you have any idea what could be changed to make it run? mri_annotation2label --labelbase ./ --lobesStrict frontal --subject fsaverage --hemi lh subject = fsaverage annotation = aparc hemi = lh labelbase = ./ surface = white Reading surface /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS60/fsaverage/surf/lh.white Loading annotations from /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS60/fsaverage/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 MRISmergeAnnotations: parcCount=11, newparcname=frontal MRISmergeAnnotations: parcCount=9, newparcname=temporal MRISmergeAnnotations: parcCount=5, newparcname=parietal MRISmergeAnnotations: parcCount=4, newparcname=occipital MRISmergeAnnotations: parcCount=4, newparcname=cingulate could not write annot file /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS60/fsaverage/surf/../label/lh.frontal.annot Permission denied Thanks in advance, Richard

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mri_vol2surf wrong hemisphere
by Defenderfer, Matthew K 01 Dec '17

01 Dec '17

Hi, I have a strange issue I can't figure out. I am currently trying to use the parcellation from Gordon et al. 2014 (download link here<http://www.nil.wustl.edu/labs/petersen/Resources.html>) to create ROIs for the frontoparietal network. They provided a volume of the parcellation in MNI152 space for public use. I took this volume and applied the mri_vol2surf command to it to create 2 overlays of the parcels, 1 for each hemisphere. The code was: mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage --mni152reg --o lh.Parcels_fsaverage_111.mgh --hemi lh mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage --mni152reg --o rh.Parcels_fsaverage_111.mgh --hemi rh The code ran, but the LH parcels in the volume were transferred to the RH on the surface and vice versa. This is a problem since the parcellation is not symmetric across hemispheres.This is not a problem with the volume either as I looked at it overlayed with the MNI152 brain in fslview and saw that the parcels were on the correct hemisphere. Another problem is that 1 of the frontoparietal parcels, number 24, was not found on the surface of either hemisphere after turning it to a surface. I don't know why this would be the case since there are all cortical parcels. I have also tried this with a volume ROI that is only located on the left hemisphere. After running essentially the same vol2surf command as above, the ROI only appeared on the RH surface. I am using mri_vol2surf from Freesurfer v6.0.0 Any help would be greatly appreciated. Thank you! Best, Matthew Defenderfer Matthew K. Defenderfer B.S. | Graduate Research Assistant Graduate Biomedical Sciences | Neuroscience UAB | The University of Alabama at Birmingham Laboratory of Kristina Visscher, PhD Department of Neurobiology CIRC 111 | C: (865) 805-6389

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transformation matrix
by John Anderson 01 Dec '17

01 Dec '17

Dear FS experts, Is there any transformation matrix between the files /mri/orig.mgz and the file /mri/rawavg.mgz Please advice! John

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FA to MNI
by John Anderson 01 Dec '17

01 Dec '17

Dear Freesurfer experts, I want to register FA map in subject space to MNI. How can I do it using freesurfer tools? Any advice is highly appreciated! J

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