Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

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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[Re] medial wall label in Freesurfer 6
by M del Mar Velasco 01 Dec '17

01 Dec '17

Hello, I have upload the data. Recipient mail was AHOOPES(a)mgh.harvard.edu. Please, check you have received it. Thanks very much, M del Mar

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Intracranial Volume
by Tamara Tavares 01 Dec '17

01 Dec '17

Hello, Just a quick question regarding the computed intracranial volume. I have ran Freesurfer version 5.1 and I have been using the intracranial volume from the aseg.stats file to correct for head size. I just want to ensure this is where I get the intracranial volume from. Thank you in advance for your help. Best, Tamara

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hippocampus subfields
by 郑凤莲 01 Dec '17

01 Dec '17

Hi professor, I am using Freesurfer for DTI data. When I run 'mri_segstats', I got the result that there was an obvious difference in left hippocampus, but no difference in right hippocampus. Then, I run segmentation of hippocampus subfields. The result showed there is no difference in total left or right hippocampus, and only in two right hippocampus subfields has significant difference. Why is there inconsistent result in two means? Thank you very much. Sincerely, Zheng

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Merging two groups
by Ramesh Babu 01 Dec '17

01 Dec '17

Hi, I have done recon-all -all processing for 2 groups in separate subjects directories. I want to put all subjects in one dkirectory. Should I copy paste all subject’s folders in one directory or is there any others steps to merge? Thanks in advance RB

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