Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

atlas space question
by Lindsay Casmaer 06 Sep '07

06 Sep '07

Hello, Are the calculated volumes for the subcortical segmentations in atlas space? I am trying to verify if the registration is done in atlas and then rolled back to subject/native space, or if the volumes are calculated in atlas space. Thanks, Lindsay

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strange values in sig.mgh file
by Rafael Huber 06 Sep '07

06 Sep '07

Hy there We did a group analysis and some results were ok (like area, thickness), but others were not. When we tried to load the sig.mgh file of the volume measures the whole hemisphere was completly yellow and the vertices were much too large. We did the whole process with the files we got from the matlab command Bruce Fischl recommended us days before. (*) Meancurv was also not correct for both hemispheres, even if i did the same for lh and rh. (in the folder rh.Turner_meancurv.glmdir is only a mri_glmfit.log file) Thanks for every help! Best regards Rafael Huber - University Zurich (*) [thickness, f] = read_curv('lh.thickness') ; [area, f] = read_curv('lh.area') ; volume = thickness .* area; save_mgh(volume, 'lh.volume.mgz', eye(4)); [thickness, f] = read_curv('rh.thickness') ; [area, f] = read_curv('rh.area') ; volume = thickness .* area; save_mgh(volume, 'rh.volume.mgz', eye(4))

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(no subject)
by Steven Scholte 05 Sep '07

05 Sep '07

Dear All, I have been trying to apply tkregister to our FEAT data as registration using automatic FLIRT does not work accurately when only a couple of functional slices are recorded. I use the option --fslregout to create a FSL compatible transformation matrix, registering the example_funct to the subjects' highres brain. I use the following: tkregister2 --feat pp0009.feat --subject pp0009 --fstarg --targ brain --fslregout fslregoutpp0009 After the manual alignment I check the registration by first applying the transformation on the example_func with FLIRT as follows: /usr/local/fsl/bin/flirt -in /ext_drv/Weibull/test/pp0009.feat/example_func.nii.gz -applyxfm -init /ext_drv/Weibull/test/fslregoutpp0009.mat -out /ext_drv/Weibull/test/pp0009.feat/example_func_TRANS.nii.gz -paddingsize 0.0 -interp trilinear -ref /ext_drv/Weibull/test/pp0009.feat/reg/highres.nii.gz Fslview will not load this resulting image though, giving me the message: Error:: FslReadTimeSeries: voxel outside valid range Does anyone know what i did wrong? Any suggestion would be helpful. Regards, Steven

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cortical flattening
by Valentin Piech 05 Sep '07

05 Sep '07

Hi all, I think that there is a bug in mris_flatten of freesurfer version 4.0.0. It took more than 1000 iterations for each occiput patch of a subject, and they are getting flattened incorrectly. I went back to version 3.0.5, and the exact same patches are flattened correctly withing 200 - 300 iterations. I can upload pictures of the patches if you would like. Best, Valentin -- Valentin Piech, Graduate Fellow Gilbert Lab for Neurobiology & Reeke Lab for Biological Modelling Rockefeller University

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cortical flattening
by Natalia Bilenko 05 Sep '07

05 Sep '07

Hi all, I am having some trouble with creating cortical patches for one subject. Though 3d patches look normal, they are not getting flattened correctly, and mris_flatten takes an unusually long time. I tried re-creating the patches (both making new 3d patches and re-running mris_flatten), but I keep getting the same problem. The patches are very oddly shaped, and the curvature pattern on the full patches looks very bizarre. The subject's data is in /space/annecy_014/kdevaney/structurals/subj20. The names of 3d patches are lh.full.patch1.3d, rh.full.patch1.3d, lh.occ.patch1.3d, and rh.occ.patch1.3d, and the names of the flat patches are lh.full.patch1.flat, rh.full.patch1.flat, lh.occ.patch1.flat, and rh.occ.patch1.flat. Any suggestions? Thanks! Natalia

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searching for a method of declaring spherical ROIs in the volume
by Avram Holmes 05 Sep '07

05 Sep '07

All, I'm attempting to create some spherical ROIs around peak activated voxels in the volume. Is there anything similar to the label dilate function for use in the volume? Thanks for any help you can offer, Avram -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes(a)fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

2 1

Subgenual problems
by Alex Fornito 05 Sep '07

05 Sep '07

Hi all, I've been having problems getting accurate surfaces in the subgenual cingulate region, as illustrated in the attached pics. I previously posted to the list about this, and you sent me a newer mris_surf for an older version of freesurfer that fixed the problem in some, but not all cases. It seems like the new version (included with 4.0) is still giving me some grief. Any suggestions re: what I can do? Thanks for your help, Alex Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre Department of Psychiatry The University of Melbourne Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 2 & 3, 161 Barry St Carlton South Vic 3053 Australia Phone: +61 3 8344 1861 Fax: +61 3 9348 0469 Email: fornitoa(a)unimelb.edu.au www.psychiatry.unimelb.edu.au/mnc

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unpacksdcmdir error
by Akram Bakkour 04 Sep '07

04 Sep '07

when I unpack a single run I get an error which I've never encountered before. I get the same error in std and dev cd /space/madrc/1/users/MADRC_ARCHIVE/MGH_MADRC_ARCHIVE/MGH_MADRC_ARCHIVE_BAY4 unpacksdcmdir -src 08242007_4TT_clindem93/dicom -targ 08242007_4TT_clindem93/raw -run 15 MEMPRAGE mgz MEMPRAGE.mgz here is the end of the output Run 15 ----------------------------------------- Tue Sep 4 11:52:48 EDT 2007 15 MEMPRAGE mgz MEMPRAGE.mgz mri_convert 08242007_4TT_clindem93/dicom/00140001 08242007_4TT_clindem93/raw/MEMPRAGE/015/MEMPRAGE.mgz --sdcmlist 08242007_4TT_clindem93/raw/MEMPRAGE/015/flf -ot mgz --nspmzeropad 3 --in_type siemens_dicom ERROR: mri_convert child killed: segmentation violation when I run mri_convert 08242007_4TT_clindem93/dicom/00140001 08242007_4TT_clindem93/raw/MEMPRAGE/015/MEMPRAGE.mgz --sdcmlist 08242007_4TT_clindem93/raw/MEMPRAGE/015/flf -ot mgz --nspmzeropad 3 --in_type siemens_dicom I get this ERROR: cannot extract sDiffusion.alBValue[1] from 08242007_4TT_clindem93/dicom/00140001 Segmentation fault Any suggestions? Thanks! Akram. -- Akram Bakkour Gerontology Research Unit 149 13th Street, Suite 2691 Charlestown, MA 02129 tel: 617-726-5571 fax: 617-726-5760 web: http://www.dickersonlab.org

2 2

mri convert
by eozdemir＠nmr.mgh.harvard.edu 04 Sep '07

04 Sep '07

When I try to convert dicoms to spm format, I get the following error which I have not encountered before. I get the same error for both anatomical dicoms and functionals. "ERROR: cannot extract sDiffusion.alBValue[1] from anat/374000-2-1.dcm Segmentation fault" Does anybody know how I can fix this? Thanks Elif

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a white matter mask that excludes sub-cortical structures
by bell0368＠umn.edu 04 Sep '07

04 Sep '07

Hello, I am trying to create a white matter mask that excludes sub-cortical structures for use in calculating FA from a dti scan. I am still using version 3.0.5 for now. I was considering combining the surface white matter mask and the aseg mask of the sub-cortical structures, but was not sure if this was valid. I am concerned because the surfaces are calculated separetly from the aseg and there will likely be some areas of disagreement between the two, for example in the hippocampus. Any suggestions would be appreciated. Does the new version 4.0.0 dti package include any helpful tools? Chris Bell University of Minnesota

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