[Freesurfer] System requirements.
Hello All, I have a P4 1.5 GHZ, 1GB ram, 65GB hard disk running redhat fedora core release 5. I am planning to install the latest version of freesurfer on it. It will be a dedicated system for a small study with the only task of processing the data on freesurfer. Will this work? I understand that it will be slow, but are there any chances of installation not working just because of hardware qualifications? Thank you, Dhruman D. Goradia (M.S.) Research Specialist. Western Psychiatric Institute and Clinic. 3811 O'Hara St. Suite 431 Pittsburgh, PA 15213 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] aseg label
Hello, I am trying to identify structures around a hippocampus using the labsl in aparc+aseg.img and FreeSurferColorLUT.txt. I see some structures labeled with 238, 232, 248 and I can't find these numbers on FreeSurferColorLUT.txt. Is there different table for aparc+aseg.mgz than one for aseg.mgz? Thank you. Nayoung ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] aseg label
When you load it as a segmentation in tkmedit, what name do those voxels get? You cann also try loadining the aparc+aseg as the -aux volume in tkmedit. The value indicated in the tkmedit control window will be the index into the color table. On Wed, 11 Apr 2007 [EMAIL PROTECTED] wrote: Hello, I am trying to identify structures around a hippocampus using the labsl in aparc+aseg.img and FreeSurferColorLUT.txt. I see some structures labeled with 238, 232, 248 and I can't find these numbers on FreeSurferColorLUT.txt. Is there different table for aparc+aseg.mgz than one for aseg.mgz? Thank you. Nayoung ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] func2tal
Do you want to register them or reslice them? What common space? We use mni305. What version of freesurfer are you using? Usually, you would register (not reslice) your bold to your freesurfer anatomical. As part of the freesurfer recon, the anat is registered (not resliced) to mni305, and running mri_vol2vol --fstal will use both registrations to reslice to mni305. doug On Mon, 9 Apr 2007, Alessandro Gagliardi wrote: I'm trying to regester my BOLD images to a common space. I tried func2tal but I got ERROR: only selxavg, selavg, and sfa functypes are currently supported. When I try to run mri_vol2vol --fstal, it expects talmni305 in my subjects directory which I don't have. Did I miss a step in the installation? Should I have talmni305 and if so, where can I get it? Otherwise, is there a new version of func2tal that accepts bshort (or other) volumes as input? Or perhaps there is another way to get my 4D data into talairach space altogether? Thanks, -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical thickness problem
It sounds like you need to change the tksurfer color scale to give it more dynamic range. On Wed, 11 Apr 2007, burak ozkalayci wrote: Dear surfers, I ran the recon-all -s bert -autorecon1 recon-all -s bert -autorecon2 recon-all -s bert -autorecon3 commands and all of them finished without any error. The log files of the commands and the file list of the resultant bert folder are attached to the mail. I can see the surface of the pial and the white with the tksurfer and try to load the ?h.thickness files as curvature files to the surfaces. But I only get fully red colored surface. What may be wrong? Also how can I read the ?h.thickness files manually to check is there any meaningful information there. The curvature maps are working but the thickness is not working. The snapshots of the the thickness and curvature are also attached. For the next step I want to ask one more question. In a previous mail in the list it is said that we compute the closest vertex on the pial from each vertex on the white, and visa-versa, then set the thickness to the average of the two. for the thickness calculation. I understand from this statement that the thickness is just measured for the surface vertices but not for the voxels in the original volume. For voxel based morphometry do you have any advice to get thickness values for the voxels of the grey matter? Thanks in advance for any advice and reply. Burak -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical thickness problem
Hi Burak, it's all red because the red/green inflection point is at 0. You need to change it for the thickness to show up well (set it the midpoint at 2 or so). And no, the thickness is a property of the surface(s), so you can't make voxel maps of it Bruce On Wed, 11 Apr 2007, burak ozkalayci wrote: Dear surfers, I ran the recon-all -s bert -autorecon1 recon-all -s bert -autorecon2 recon-all -s bert -autorecon3 commands and all of them finished without any error. The log files of the commands and the file list of the resultant bert folder are attached to the mail. I can see the surface of the pial and the white with the tksurfer and try to load the ?h.thickness files as curvature files to the surfaces. But I only get fully red colored surface. What may be wrong? Also how can I read the ?h.thickness files manually to check is there any meaningful information there. The curvature maps are working but the thickness is not working. The snapshots of the the thickness and curvature are also attached. For the next step I want to ask one more question. In a previous mail in the list it is said that we compute the closest vertex on the pial from each vertex on the white, and visa-versa, then set the thickness to the average of the two. for the thickness calculation. I understand from this statement that the thickness is just measured for the surface vertices but not for the voxels in the original volume. For voxel based morphometry do you have any advice to get thickness values for the voxels of the grey matter? Thanks in advance for any advice and reply. Burak ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical thickness problem
Burak, The file bert/stats/?h.aparc.stats contains thickness data for parcellated regions. You can get the raw thickness data with: mris_convert -c lh.thickness lh.white lh.thickness.asc where lh.thickness.asc will contain: vertex x y z thickness in mm noting that the x,y,z pertains to the lh.white surface. Nick On Wed, 2007-04-11 at 18:46 +0200, burak ozkalayci wrote: Dear surfers, I ran the recon-all -s bert -autorecon1 recon-all -s bert -autorecon2 recon-all -s bert -autorecon3 commands and all of them finished without any error. The log files of the commands and the file list of the resultant bert folder are attached to the mail. I can see the surface of the pial and the white with the tksurfer and try to load the ?h.thickness files as curvature files to the surfaces. But I only get fully red colored surface. What may be wrong? Also how can I read the ?h.thickness files manually to check is there any meaningful information there. The curvature maps are working but the thickness is not working. The snapshots of the the thickness and curvature are also attached. For the next step I want to ask one more question. In a previous mail in the list it is said that we compute the closest vertex on the pial from each vertex on the white, and visa-versa, then set the thickness to the average of the two. for the thickness calculation. I understand from this statement that the thickness is just measured for the surface vertices but not for the voxels in the original volume. For voxel based morphometry do you have any advice to get thickness values for the voxels of the grey matter? Thanks in advance for any advice and reply. Burak ___ 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] Manuals and Scuba
Dear FreeSurfer Team I'm a new user of freesurfer and I would like to ask you few questions. 1.Where can I find more information regarding SCUBA? 2.I read very carefully through the freesurfer website, (all the work flow and tutorials) however, I was wondering weather every time I do any kind of changes, do I have to run recon all again,, or there are any single commands that repair/edit my own revisions? 3. What is the newest version of the FreeSurfer Manual and where can I find it Thank You in advance Sharon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Manuals and Scuba
1.Where can I find more information regarding SCUBA? https://surfer.nmr.mgh.harvard.edu/fswiki/Scuba 3. What is the newest version of the FreeSurfer Manual and where can I find it The freesurfer wiki at that address is our current live documentation. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Volumes for labels
Hi, I was just wandering exactly how the grey matter volume for a given label is calculated in mris_anatomical_stats. Multiplying the average thickness by the area estimate I get in the output file does not give me exactly the same estimate of grey matter volume as what mris_anatomical_stats returns. Is the mris_anatomical_stats volume estimate calculated on a vertex-by-vertex basis? Thanks, Alex Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre National Neuroscience Facility The University of Melbourne Levels 2 3, 161 Barry St Carlton South 3053 Vic Australia Ph: +61 3 8344 1861 Fax:+61 3 9348 0469 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
