Re: [Freesurfer] Re: Leopard is missing mri_segstats

Hi Nick This link does not work properly. Does the missing of these two files affect the normal recon-all -all processing stream? Regards Juergen On 2.12.2008 5:24 Uhr, "Nick Schmansky" <[EMAIL PROTECTED]> wrote: > ftp:/surfer/nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/macintel-

[Freesurfer] recon-all rerun

Hi, I ran recon-all -all crashed for reasons unrelated to FreeSurfer. I re-ran the analysis without -clean. Is the new skull stripped volume stored in brainmask.auto.mgz instead of brainmask.mgz? Thanks, Gabi ___ Freesurfer mailing list Freesurfer@nmr.

[Freesurfer] Re: Leopard is missing mri_segstats

Hans, I've posted those two binaries here: ftp:/surfer/nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/macintel-leopard Nick On Mon, 2008-12-01 at 15:07 -0600, Hans Johnson wrote: > It appears that the program mri_segstats is missing under version 4.1 of > mac. > > diff ~/MacLeopar

Re: [Freesurfer] Segmentation Volume Data

Hi Mishkin, the partial volume correction considers every voxel that borders a voxel with a different label. It then computes what other label is it's most common nbr, then computes the mean non-border intensity for the central and nbr labels in a window (7x7x7 I think), and uses these two mea

RE: [Freesurfer] RE: for cortical thickness

Hi Nick, Thank you very much for your help in the previous email. Recently, I read and thought your manual very carefully and tried some other ways. The first one: I tried to transfer ROI5.nii directly to subject's surface (not via fsaverage). i.e., cd $SUBJECTS_DIR/subjid/surf Fslregister --

[Freesurfer] Possible to constrain FDR to a label in the volume?

Dear FreeSurfers, I've created a basal ganglia label and am wondering if it's possible to constrain the FDR calculation to that label? Based on earlier messages it seems like tksurfer has a "marked label only" option for FDR, but I haven't been able to find something similar in tkmedit. Any hel

Re: [Freesurfer] Segmentation Volume Data

Hi, Are the details of the partial volume corrections described anywhere on the wiki, I couldn't find anything? Is it just a certain percentage of the volume that is disregarded depending on the surface area, or is there a probabilistic labeling of the structures somewhere? Is it possible to get a

[Freesurfer] Leopard is missing mri_segstats

It appears that the program mri_segstats is missing under version 4.1 of mac. diff ~/MacLeopard.list ~/Linux64.list 38a39 > /opt/freesurfer/bin/3dvolreg 62a64 > /opt/freesurfer/bin/dmri_poistats 77a80 > /opt/freesurfer/bin/flirt.newdefault.20080811.sch 79a83,84 > /opt/freesurfer/bin/freeview > /o

Re: [Freesurfer] atlas use

Nurunisa, Yes, you can add just -gca GCA_ALL to the command line, but you will need to also need to add -no-wsgcatlas to recon-all, because the skull- stripping step uses the gca_withskull atlas. For added measure, if you only want to use your own atlas, you might want to move or rename the RB_al

[Freesurfer] atlas use

Hi, if I want to use an alternative subcortical atlas (and I only have the equivalent of GCA_ALL but not GCA_SKULL), can I just add -gca GCA_ALL to the command line? Is there anything else I need to do? thanks, Nurunisa ___ Freesurfer mailing list Fr