Re: [Freesurfer] Trans. : VBM question

Hi Mohamed Doug is away this week and can give you a more details answer next week. Certainly you could use mris_anatomical_stats -l to compute the volume/thickness/area for each subject then do whatever GLM analysis you want outside of FS. cheers Bruce On Fri, 3 Nov 2017,

[Freesurfer] Trans. : VBM question

Dear All, Does anyone have an answer to the following VBM question? Many thanks in advance, Regards -Mail original- De: "Mohamed Ali Bahri" À: "Freesurfer support list" Envoyé: Jeudi, Novembre 2, 2017 06:08:33 PM Objet:

Re: [Freesurfer] Occipital flattening

why are you including the -1 flag? You only need that if you have only a single surface (that is, it's not a standard freesurfer recon dir). Try removing it On Fri, 3 Nov 2017, Patricia Stefancin wrote: ls -l *patch*  output: -rw-rw-r-- 1 tstefancin analyses 723208 Oct 26 14:38

Re: [Freesurfer] Occipital flattening

ls -l *patch* output: -rw-rw-r-- 1 tstefancin analyses 723208 Oct 26 14:38 lh.occip.patch3d -rw-rw-r-- 1 tstefancin analyses 646376 Oct 27 09:32 lh.occip.patch.3d -rw-rw-r-- 1 tstefancin analyses 401704 Oct 26 14:25 lh.patch -rw-rw-r-- 1 tstefancin analyses 917832 Oct 26 14:40 rh.occip.patch3d

Re: [Freesurfer] Occipital Flattening

Hi Patricia to help you we always need the full command line and screen output of what you ran. In this case you should also include the output of pwd and ls -l . cheers Bruce On Fri, 3 Nov 2017, Patricia Stefancin wrote: I managed to change the directory, but when I ran the

Re: [Freesurfer] Occipital Flattening

I managed to change the directory, but when I ran the mris_flatten command it still said the file could not be found. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] mris_apply_reg

Hi Lanbo, You need Freesurfer 6 to run this command. The flag --src-label is not part of FS5.3 Best, M_ From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of lanbo Wang Sent: Friday, November 3, 2017 11:49 AM To:

Re: [Freesurfer] mris_apply_reg

Hi Lanbo Doug (who knows the answer to this question) is on vacation. Can you repost next week? thanks Bruce On Fri, 3 Nov 2017, lanbo Wang wrote: Dear Freesurfer experts, I try run this code according to Xhemi： mris_apply_reg --src-label label/rh.V1_exvivo.thresh.label --trg

[Freesurfer] mris_apply_reg

Dear Freesurfer experts, I try run this code according to Xhemi： mris_apply_reg --src-label label/rh.V1_exvivo.thresh.label --trg rh-on-lh.V1_exvivo.thresh.label \ --streg xhemi/surf/lh.fsaverage_sym.sphere.reg surf/lh.fsaverage_sym.sphere.reg However, error shows: Option --src-label unknown.

[Freesurfer] RE : Occipital Flattening

When I run the command pwd it shows me as being in the home file, but I have repeatedly changed the directory to the subject's surf folder. Why is it not changing the directory? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Occiptial flattening

what directory were you in? That is, what is the output of the command pwd if not the subject's surf dir you need to specify the path to the patch file on the command line cheers Bruce On Fri, 3 Nov 2017, Patricia Stefancin wrote: > Hi again,I ran the command you send and the output is as

Re: [Freesurfer] Occiptial flattening

Hi again, I ran the command you send and the output is as follows ls cannot access *patch* : no such file or directory ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] Occipital flattening

Hi Patricia what directory are you in when you run that command? If the subject's surf dir, can you then run: ls -l *patch* and send us the output? Bruce On Fri, 3 Nov 2017, Patricia Stefancin wrote: Hi Bruce,Here is the command line and the output.  mris_flatten -1 -w 0 -distances 20

Re: [Freesurfer] Occipital flattening

Hi Bruce, Here is the command line and the output. mris_flatten -1 -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat MRISread(lh.occip.patch.3d): could not open file No such file or directory mris_flatten: could not read surface file lh.occip.patch.3d No such file or directory