Re: [Freesurfer] Re: Freesurfer Digest, Vol 41, Issue 13-add gray matter
Thank great helps from the group. I have a related issue. In my images some gray matters at the top of medial wall is lass than 60, so that these small areas are not included in gray matter. This may be due to the shadow of RF coil. Can I fix it by either decrease the threshold of gray matter or manually include these small areas? Thank you again, Xin Bruce Fischl Mon, 09 Jul 2007 15:08:20 -0700 usually it's because the bias field brings the gm too low, so if you find nearby white matter (that is *not* partial volumed) that is below 110, putting some control points there will also move the pial surface out a bit. Or the skull strip could have removed it. Or the topology fixer might have done something strange. This can be checked by looking at the ?h.orig.nofix surface and seeing if it is more accurate than the ?h.orig. If this is the case you'll need to identify and correct the topological defect in the wm.mgz volume. cheers, Bruce On Mon, 9 Jul 2007, Sebastian Moeller wrote: Hi, not being an expert, please take my rambling with a grain of salt. But I am somewhat curious to learn better ways ;) On Jul 9, 2007, at 11:03 PM, [EMAIL PROTECTED] wrote: Message: 9 Date: Mon, 9 Jul 2007 17:01:42 -0400 From: "Wang, Xin" <[EMAIL PROTECTED]> Subject: [Freesurfer] add the gray matter To: "freesurfer" Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hello, Group I need to edit the pial surface. I learned to remove points with tkmedit from the tutorial. But how to add gray matter in the pial surface? 1) If you have nothing where gray matter should be, then check brainmask.mgz, if this is missing gray matter, around where your problems occur edit the bainmask.mgz volume and pick up your reconstruction from there. (IIRC there is something in the tutorial about this) 2) If there is white matter where gray matter should be, be sure to to check nu.mgz and brainmask.mgz at the critical parts for too high intensity in the supposed gray matter. Either control points might helo (unlikely) or redoing the intensity correction (and then starting again from that point). At least for my data, acquired with surface coils, sub-optimal intensity correction is really annoying. ahoi & good luck Sebastian Thank you in advance. Xin -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/ attachments/20070709/591cc54f/attachment.html -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 41, Issue 13 ** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Validation for surfaces
Hi, regarding validation of freesurfer's surface reconstructions, I was just wondering which papers you would most recommend citing. Thanks, -Aaron- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Validation for surfaces
Hi Aaron, if you look at the reprints on our wiki there are a couple you could cite, but the recent one with Xiao Han as the first author is probably the most relevant. cheers Bruce On Mon, 20 Aug 2007, Goldman, Aaron (NIH/NIMH) [C] wrote: Hi, regarding validation of freesurfer's surface reconstructions, I was just wondering which papers you would most recommend citing. Thanks, -Aaron- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] surface DTI group contrast
Hello, I have been attempting to run a between group DTI contrast using glmfit, and it could not determine how to produce the data that is given to mri_glmfit as its input. My approach below may be wrong, so if you can recommend a better way of doing it please advise. Assuming this method is a valid approach, here is my technical problem: the resampling step shown below seems to work, but glmfit reports that there is an incorrect number of rows, so I guess something goes wrong. The first thing I do is resample from volume to surface onto average7 for each of the subjects: cat Subject_Lists/bw-group-error-dti-5 | while read sub ; do mri_vol2surf \ --src "$sub"/dti/unwarp/maps/sreg/fa.bhdr \ --srcreg "$sub"/bold/register.dat \ --trgsubject average7 \ --out DTI_HCvASD_mriglfmit/surface/"$sub"_fa.mgh \ --hemi lh done And then I create a final output to give to mri_glmfit: mri_concat DTI_HCvASD_mriglfmit/surface/mano*_fa.mgh --o DTI_HCvASD_mriglfmit/all_fa.mgh The process I'm attempting above is similar to what mris_preproc uses surf2surf to do, but I think I need to use vol2surf instead of surf2surf. As far as I can tell mris_preproc would not work, because in what I am doing I need to go from the volume to the surface. This vol2surf method "works" in that it doesn't have any errors when running (though some warnings about registration file being different from source file), and it generates the resampled surface that I concatenate at the end. So far so good but when I run mri_glmfit, I get an error message (see below). mri_glmfit \ --really-use-average7 \ --y DTI_HCvASD_mriglfmit/all_fa.mgh \ --fsgd fsgd_and_contrast_files/BwGroupErrorDTI5.fsgd \ --glmdir DTI_HCvASD_mriglfmit/HCvASD.fsfast.glmdir \ --C fsgd_and_contrast_files/BwGroupErrorDTI5.mat sysname Linux hostname vantz machine x86_64 user levy FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y/autofs/space/ventzl_015/users/DTI_HCvASD_mriglfmit/all_fa.mgh logyflag 0 usedti 0 FSGD fsgd_and_contrast_files/BwGroupErrorDTI5.fsgd glmdir DTI_HCvASD_mriglfmit/HCvASD.fsfast.glmdir DoFFx 0 Creating output directory DTI_HCvASD_mriglfmit/HCvASD.fsfast.glmdir Loading y from /autofs/space/ventzl_015/users/DTI_HCvASD_mriglfmit/all_fa.mgh Matrix condition is 1 Pruning voxels by frame. Found 155495 voxels in mask Saving mask to DTI_HCvASD_mriglfmit/HCvASD.fsfast.glmdir/mask.mgh search space = 155495 *ERROR: dimension mismatch between y and X. y has 23 inputs, X has 24 rows. * My .fsgd file matches the exact set of subjects that went into the aggregate .mgh file, so that isn't the reason. What do you think might be the cause of this error? Thanks, Rob Also, here is some information on the environment I ran these commands in: freesurfer-Linux-centos4_x86_64-dev-20070819 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/dev FSFAST_HOME /usr/local/freesurfer/dev/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR MNI_DIR /usr/local/freesurfer/dev/mni FSL_DIR /usr/local/freesurfer/dev/fsl [vantz:SUBJECTS_DIR] (nmr-dev-env) pwd /space/ventzl/1/users/SUBJECTS_DIR -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 Charlestown, MA 02129 email: [EMAIL PROTECTED] phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] surface DTI group contrast
Hi, no need for a reply to this (I should have waited a little longer before posting to the list). I found a good example of how do it using mri_preproc, and that worked (as determined by comparison with known correct results). -Rob Robert Levy wrote: Hello, I have been attempting to run a between group DTI contrast using glmfit, and it could not determine how to produce the data that is given to mri_glmfit as its input. My approach below may be wrong, so if you can recommend a better way of doing it please advise. Assuming this method is a valid approach, here is my technical problem: the resampling step shown below seems to work, but glmfit reports that there is an incorrect number of rows, so I guess something goes wrong. The first thing I do is resample from volume to surface onto average7 for each of the subjects: cat Subject_Lists/bw-group-error-dti-5 | while read sub ; do mri_vol2surf \ --src "$sub"/dti/unwarp/maps/sreg/fa.bhdr \ --srcreg "$sub"/bold/register.dat \ --trgsubject average7 \ --out DTI_HCvASD_mriglfmit/surface/"$sub"_fa.mgh \ --hemi lh done And then I create a final output to give to mri_glmfit: mri_concat DTI_HCvASD_mriglfmit/surface/mano*_fa.mgh --o DTI_HCvASD_mriglfmit/all_fa.mgh The process I'm attempting above is similar to what mris_preproc uses surf2surf to do, but I think I need to use vol2surf instead of surf2surf. As far as I can tell mris_preproc would not work, because in what I am doing I need to go from the volume to the surface. This vol2surf method "works" in that it doesn't have any errors when running (though some warnings about registration file being different from source file), and it generates the resampled surface that I concatenate at the end. So far so good but when I run mri_glmfit, I get an error message (see below). mri_glmfit \ --really-use-average7 \ --y DTI_HCvASD_mriglfmit/all_fa.mgh \ --fsgd fsgd_and_contrast_files/BwGroupErrorDTI5.fsgd \ --glmdir DTI_HCvASD_mriglfmit/HCvASD.fsfast.glmdir \ --C fsgd_and_contrast_files/BwGroupErrorDTI5.mat sysname Linux hostname vantz machine x86_64 user levy FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y/autofs/space/ventzl_015/users/DTI_HCvASD_mriglfmit/all_fa.mgh logyflag 0 usedti 0 FSGD fsgd_and_contrast_files/BwGroupErrorDTI5.fsgd glmdir DTI_HCvASD_mriglfmit/HCvASD.fsfast.glmdir DoFFx 0 Creating output directory DTI_HCvASD_mriglfmit/HCvASD.fsfast.glmdir Loading y from /autofs/space/ventzl_015/users/DTI_HCvASD_mriglfmit/all_fa.mgh Matrix condition is 1 Pruning voxels by frame. Found 155495 voxels in mask Saving mask to DTI_HCvASD_mriglfmit/HCvASD.fsfast.glmdir/mask.mgh search space = 155495 *ERROR: dimension mismatch between y and X. y has 23 inputs, X has 24 rows. * My .fsgd file matches the exact set of subjects that went into the aggregate .mgh file, so that isn't the reason. What do you think might be the cause of this error? Thanks, Rob Also, here is some information on the environment I ran these commands in: freesurfer-Linux-centos4_x86_64-dev-20070819 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/dev FSFAST_HOME /usr/local/freesurfer/dev/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR MNI_DIR /usr/local/freesurfer/dev/mni FSL_DIR /usr/local/freesurfer/dev/fsl [vantz:SUBJECTS_DIR] (nmr-dev-env) pwd /space/ventzl/1/users/SUBJECTS_DIR -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 Charlestown, MA 02129 email: [EMAIL PROTECTED] phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 Charlestown, MA 02129 email: [EMAIL PROTECTED] phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
