[Freesurfer] Recon-all
Dear Freesurfers. I am facing a crucial point.:)and I need your help. After examining most of our subjects, we decided that there is no need to run all the procedures- work flow, since our data is not prone to too many failures, and just start with recon-all-all, get all the data and then start editing. Usually we have to add very few cp and to do some pial edits (not in all the cases).However, our talairach looks good, no skull striping problems and wm is also ok. I was wondering if running recon-all-all, and then fixing the i.e. cp , or the pial surface when repeating autorecon2-cp, or autorecon2-pial-autorecon3, is it harmful? Does this mass my analysis , or it's ok? Thank You Sharon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Partitioning GM/WM boundary surface
Thanks Bruce, From the ReconAllDevTable I see mris_make_surfaces -mgz -w 0 -T1 brainfinalsurfs.mgz $subject $hemi which will produce new ?h.thickness, area, curv, white and pial surfaces as well. Are these the options I should rerun with? Cheers, -Morgan Bruce Fischl wrote: rerun mris_make_surfaces and it will create them (and not deform the surface in regions outside the label) On Wed, 25 Jul 2007, Morgan Hough wrote: Hi Bruce, These subjects were run with an older version of FreeSurfer and don't have ?h.cortex.label. I am afraid I don't see a generating command in the ReconAllDevTable. In ReconAllFilesVsSteps it looks like it is coming from mris_make_surfaces. Can I generate these labels from the old recon-all output? Cheers, -Morgan Bruce Fischl wrote: Hi Morgan, yes, that seems reasonable. You can start with the ?h.cortex.label and subdivide it into sulcal and gyral to avoid the medial wall. cheers, Bruce On Tue, 24 Jul 2007, Morgan Hough wrote: I would like to obtain a ratio of gyral/sulcal GM/WM boundary surface area. I was wondering if the best solution would be to threshold each subject's ?h.sulc files to form a label that contains all gyral areas and then use mris_anatomical_stats -l to constrain a surface area measurement to this label? I was also wondering if there is a simple way to exclude the medial wall area from consideration in these calculations? Thanks in advance for your time. Cheers, -Morgan ___ 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
Re: [Freesurfer] Partitioning GM/WM boundary surface
Morgan, Generally you would want to use: recon-all -finalsurfs -s subj -hemi hemi which will ensure calling mris_make_surfaces with the right parameters. Nick On Wed, 2007-07-25 at 16:59 +0100, Morgan Hough wrote: Thanks Bruce, From the ReconAllDevTable I see mris_make_surfaces -mgz -w 0 -T1 brainfinalsurfs.mgz $subject $hemi which will produce new ?h.thickness, area, curv, white and pial surfaces as well. Are these the options I should rerun with? Cheers, -Morgan Bruce Fischl wrote: rerun mris_make_surfaces and it will create them (and not deform the surface in regions outside the label) On Wed, 25 Jul 2007, Morgan Hough wrote: Hi Bruce, These subjects were run with an older version of FreeSurfer and don't have ?h.cortex.label. I am afraid I don't see a generating command in the ReconAllDevTable. In ReconAllFilesVsSteps it looks like it is coming from mris_make_surfaces. Can I generate these labels from the old recon-all output? Cheers, -Morgan Bruce Fischl wrote: Hi Morgan, yes, that seems reasonable. You can start with the ?h.cortex.label and subdivide it into sulcal and gyral to avoid the medial wall. cheers, Bruce On Tue, 24 Jul 2007, Morgan Hough wrote: I would like to obtain a ratio of gyral/sulcal GM/WM boundary surface area. I was wondering if the best solution would be to threshold each subject's ?h.sulc files to form a label that contains all gyral areas and then use mris_anatomical_stats -l to constrain a surface area measurement to this label? I was also wondering if there is a simple way to exclude the medial wall area from consideration in these calculations? Thanks in advance for your time. Cheers, -Morgan ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FS installation for FC 7 + ATI Mobility FireGL V5000 graphics card
Hi All, Does anyone have any experience with FS installation under Fedora Core 7 Linux + ATI Mobility FireGL V5000 (256K) graphics card? Which is the correct version to use? Do I need any additional patches to download or are any other configuration settings necessary? Thanks in advance, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 *** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] freediffusion dtrecon mask
Hello, [EMAIL PROTECTED] doesn't seem to exist, so I'm hoping one of you can help me out. I seem to be having trouble with the -mask 0 flag in dtrecon. It doesn't apply a brainmask! I tried -mask 1 but that didn't work either. I unpacked the data properly, then ran diff-flirt -i f -o unwarp/f -tmpdir tmp for motion and eddy current correction and then ran dtrecon -i f -o maps -mask 0 but my maps/fa volume is not brain masked. Here are the logs: /space/thigpen/10/users/min/OFRR27/dti/025/unwarp/dtrecon-22259.log /space/thigpen/10/users/min/OFRR27/dti/025/unwarp/raw2tensor-22289.log /space/thigpen/10/users/min/OFRR27/dti/025/unwarp/tensor2eig-22447.log I can see where it says Calculating background fraction ... brain is100% of volume nonbrain is 0% of volume but I still don't understand why it's not working. I even tried running dtrecon on the unpacked data without running diff-flirt, but no luck. Any and all help is highly appreciated. Thanks! Akram. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] freediffusion dtrecon mask
Hi Akram, I have access to that directory, but those logs don't seem to be there. What was the exact command you ran using dtrecon? Thanks, Dennis Akram Bakkour wrote: Hello, [EMAIL PROTECTED] doesn't seem to exist, so I'm hoping one of you can help me out. I seem to be having trouble with the -mask 0 flag in dtrecon. It doesn't apply a brainmask! I tried -mask 1 but that didn't work either. I unpacked the data properly, then ran diff-flirt -i f -o unwarp/f -tmpdir tmp for motion and eddy current correction and then ran dtrecon -i f -o maps -mask 0 but my maps/fa volume is not brain masked. Here are the logs: /space/thigpen/10/users/min/OFRR27/dti/025/unwarp/dtrecon-22259.log /space/thigpen/10/users/min/OFRR27/dti/025/unwarp/raw2tensor-22289.log /space/thigpen/10/users/min/OFRR27/dti/025/unwarp/tensor2eig-22447.log I can see where it says Calculating background fraction ... brain is100% of volume nonbrain is 0% of volume but I still don't understand why it's not working. I even tried running dtrecon on the unpacked data without running diff-flirt, but no luck. Any and all help is highly appreciated. Thanks! Akram. ___ 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
Re: [Freesurfer] Partitioning GM/WM boundary surface
yes, I think -aseg is the default now, so you don't need to specify it (it uses the aseg to figure out what's cortex and what's not) On Wed, 25 Jul 2007, Morgan Hough wrote: Thanks Bruce, From the ReconAllDevTable I see mris_make_surfaces -mgz -w 0 -T1 brainfinalsurfs.mgz $subject $hemi which will produce new ?h.thickness, area, curv, white and pial surfaces as well. Are these the options I should rerun with? Cheers, -Morgan Bruce Fischl wrote: rerun mris_make_surfaces and it will create them (and not deform the surface in regions outside the label) On Wed, 25 Jul 2007, Morgan Hough wrote: Hi Bruce, These subjects were run with an older version of FreeSurfer and don't have ?h.cortex.label. I am afraid I don't see a generating command in the ReconAllDevTable. In ReconAllFilesVsSteps it looks like it is coming from mris_make_surfaces. Can I generate these labels from the old recon-all output? Cheers, -Morgan Bruce Fischl wrote: Hi Morgan, yes, that seems reasonable. You can start with the ?h.cortex.label and subdivide it into sulcal and gyral to avoid the medial wall. cheers, Bruce On Tue, 24 Jul 2007, Morgan Hough wrote: I would like to obtain a ratio of gyral/sulcal GM/WM boundary surface area. I was wondering if the best solution would be to threshold each subject's ?h.sulc files to form a label that contains all gyral areas and then use mris_anatomical_stats -l to constrain a surface area measurement to this label? I was also wondering if there is a simple way to exclude the medial wall area from consideration in these calculations? Thanks in advance for your time. Cheers, -Morgan ___ 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
