Freesurfer

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30088 discussions

mris_smooth issue with gaussian parameters
by Marcos Martins da Silva 08 Oct '13

08 Oct '13

Hi, Freesurfers I am getting some interesting hippocampal surfaces with the following steps: 1- recon-all -all -hippo-subfields 2- mri-concat (only CA1, CA23, CA4DG and the tail complement volumes) 3- a custom OCTAVE script to segment the concatenated volume from step 2 into Head, Body and Tail 4- mri_binarize Head, Body and Tail volumes from step 3 5- mri_tessellate the binary masks from step 4 6- mri_smooth the surfaces from step 5 Using freeview I got a screenshot showing both hippocampi segmented (hipposurf3d.png is attached). This approach worked well for 16 subjects up to step 5. Step 6 was completed as well in 13 out 16 subjects. The only problem was during left hippocampal body smoothing in 3 subjects (all the other surfaces from all 16 subjects in were smoothed with no problem). For these 3 surfaces, mris_smooth simply freezes, with no error message. I must press control + C to quit the program. During the freezing I noticed high CPU use. It follows the exactly command I used and the screen output. mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippoBody lh.surfHippoBody using Gaussian curvature smoothing with norm 5.00 with 2 smooth steps averaging curvature for 1 iterations smoothing for 1 iterations smoothing surface tessellation for 1 iterations... ------------------------------------------------------ ------------------------------------------------------ ------------------ pass 1 (num=2853) ------------------ ------------------------------------------------------ ------------------------------------------------------ If I supress the gaussian parameters and run just something like: mris_smooth -nw -a 1 -n 1 surfLeftHippoBody lh.surfHippoBody or even mris_smooth -nw surfLeftHippoBody lh.surfHippoBody I got the smoothed surface with no errors but the final quality is not as good as when I use the gaussian parameters. I am attaching one of the problematic surface files so you can check it (surfLeftHippobody). Intersting if I use a surface with all left hippocampus (including head, problematic body and tail and) smoothing completes without error Thank you very much for any help. Marcos

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5.3.0, mri_segstats
by EK Kim 08 Oct '13

08 Oct '13

Dear experts, I updated FreeSurfer as a 5.3.0 version but have a problem about the missing ribbon.mgz when running recon-all procedure. I found the ftp address but couldn't find the mri_segstats. (ftp:/surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats) Could you let me know the right address of the file? Best, EK.

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Problem with DWI and structural coregistration
by stdp82＠virgilio.it 08 Oct '13

08 Oct '13

Hi list, I'm performing trac-all but I'm noting some coregistration error.I have try to run separately each step. When -masks was finished, cortex masks and other file were wrongly coregistared on DTI. In the next step also the dti_FA and other maps are wrong becouse some parts are lacking. Please see also the attachments. Thanks, Stefano

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half brain when converting into mgz
by Erik Lindberg 08 Oct '13

08 Oct '13

Dear Freesurfer experts, I analyzed a lot of brains in Freesurfer. For some reason some brains gets cut on the top (see attaced image). I cannot understand why this is happening. The dicom image is ok, but as soon as I convert it into mgz suddenly the top of the brain is cut off. Out of 60 brains with identical mri sequence 5 brains are cut. Would be grateful if you suggest how to solve this problem Thanks in advance! Olof

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Cerebellar subdivisions
by Alan Francis 07 Oct '13

07 Oct '13

Hi Bruce et al, Is the parcellation of the cerebellar subdivisions in the works for the next version of FS? Is there an ETA for this? thanks so much, Alan

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[FreeSurfer] changes to subcortical volumes
by Francesco Siciliano 07 Oct '13

07 Oct '13

Hello, After doing manual editing to the surface of a brain (brainmask.mgz, wm.mgz, and brain.finalsurfs.mgz) through freeview, I noticed that the volumes of some subcortical structures (specifically the hippocampus, amygdala, and accumbens) had changed, even though I did not edit aseg.mgz. Is that to be expected? Most of the differences were minimal, a 5% change or less. However some of the structures changed by as much as 10 or 15%. I am preparing to do a second-level analysis of ROIs of the hippocampus and amygdala on a group of subjects. Given that cortical edits seem to influence subcortical structure volumes, would it be unreliable to run a second-level analysis with subcortical volumes recorded prior to cortical editing? Thank you, -Francesco Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155

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restoring wm.mgz
by Jason Tourville 07 Oct '13

07 Oct '13

Hi there, I'm working on a project in which I manually "erased" voxels (changed to '1') in the optic chiasm region in the wm.mgz and brainmask.mgz. This was done to eliminate those voxels from the surface reconstructions. We've since realized that this isn't necessary...our results are largely unaffected by the edit. So we've skipped that edit on most (110+) scans. For the few scans that have the optic chiasm edits, I'd like to regenerate the original surfaces but would like to retain the numerous other edits I've made to the brainmask.mgz and wm.mgz volumes outside the optic chiasm region. I have tried to do this by "cloning" the voxels from the original brainmask and wm volumes to the edited version, thereby restoring the original voxel values in only this region. When I then rerun recon all from the autorecon2-cp option, the "restored" voxels in the wm volume are set set to "0" (so no longer the original values and not even the "erased" value of "1") before the surfaces are generated. The result is that the surfaces in the optic chiasm area remain "clipped." I've tried this on a couple different scans and after moving the wm.seg.mgz volume out of the mri/ directory. Any idea why this is happening? Is there a solution that does not require me to edit these scans from scratch? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

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[FreeSurfer] control points
by Francesco Siciliano 07 Oct '13

07 Oct '13

Hello, I am still having issues getting all of my control points to be effective. When I load my original point set (control.dat) and add control points to the set (using the control points edit tool), the new control points are visible but are not taken into account when I re-run recon-all (recon-all -autorecon2 -autorecon3 -s Subject1). I have also tried saving multiple control points (control2.dat, etc) and that does not seem to work either. It appears as though I am unable to add control points after saving the first set during my first edit of a brain. This is problematic because one edit of a brain is rarely sufficient, and I typically need to edit my control point set. Yet there seems to be no way to do this. The only other thing that I think may be causing the problem is that I am running freeview 5.3 and freesurfer 5.2 (to keep our data consistent with the same version). Any ideas how to resolve this issue? -Francesco Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155

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Re: [Freesurfer] Binary stats
by Douglas N Greve 07 Oct '13

07 Oct '13

Not from the mri_cluster. If you run mri_binarize --i mask.nii --count count.dat --min 0.5 the total volume of the mask will be in the count file (along with some other numbers). doug ps. Please remember to post to the list instead of me directly. thanks! On 10/07/2013 12:53 PM, pfotiad(a)nmr.mgh.harvard.edu wrote: > Hi Doug, > > Thanks for your reply. Besides getting the volume of each cluster > separately, would you happen to know a way to get the sum of the volumes > (in mm^3) of all the clusters that come out in the summary file? > > Thanks, > Panos > >> If you save a segmentation from mri_volcluster (--ocn), then you can >> feed that into mri_segstats as the segmentation and it will create >> another summary file with the volumes of each cluster >> >> doug >> >> On 10/07/2013 10:12 AM, pfotiad(a)nmr.mgh.harvard.edu wrote: >>> Hi FS Community, >>> >>> I have a binary mask and have used the mri_volcluster command to come up >>> with different clusters and their volumes based on that binary mask. >>> However, I was wondering if it would be possible to come up with the sum >>> of the sizes (in mm3) of all the different clusters that come out of the >>> sum file as well. I could do it by writing a script that reads the >>> separate values from the summary file output of the mri_volcluster and >>> then adding them, but I was wondering whether there was an easier way. >>> >>> Thanks in advance, >>> Panos >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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trouble with pial surface in v5.1
by Caspar M. Schwiedrzik 07 Oct '13

07 Oct '13

Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar

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