[Freesurfer] LGI : cannot allocate memory

Hello, Do you know why I have a memory problem with LGI ? This is my output: thanks [EMAIL PROTECTED] ~]$ recon-all -lgi -sid chuv60 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /home/cammoun/freesurfer -rwxrwxrwx 1 root root 620884 Apr 16 08:58 /usr/

[Freesurfer] LGI

Hi I am trying to launch the LGI option, but the program seems to wait for a response, here is the complete output,. Even if I type yes it doesn't seems to continue. Do you know how to solve this? Thanks in advance Leila [EMAIL PROTECTED] ~/freesurfer]# recon-all -lgi -sid chuv60 IN

[Freesurfer] bad parcellation

Hello, In some brains, the parcellation into 35 gyral based parcels is bad while the white matter seems ok, do you know how to correct this? Or what could be the raison Thanks Leila ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://ma

[Freesurfer] variability

Hello, Is there any paper talking about the variability of the used methods (on reconall )? Especially the parcellation? If I reprocess one subject 10 times with the same Freesurfer version, should I expect the same result for parcellation? The freesurfer version that I use is stable3 I trie

[Freesurfer] mris_volmask + mris_volume

Hi again, I need the command mris_volmask that I found in the website but I don't have it I my freesurfer (stable3), someone can help me? And how to use mris_volume? I wrote:mris_volume in the surf folder, after small time I can see like an output this number 333731, but I can not find any new

RE: [Freesurfer] mri_surf2vol

doesn’t work with mri_convert _ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Doug Greve Sent: mercredi, 15. août 2007 23:11 To: Leila BH Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_surf2vol Do you want a mask of just the ribbon or everything

RE: [Freesurfer] mri_surf2vol

atlab, isn't it? I was looking for something that fill the volume from the mesh for mere accuracy.. Leila -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bruce Fischl Sent: mercredi, 15. août 2007 22:03 To: Doug Greve Cc: freesurfer@nmr.mgh.harvard.edu

[Freesurfer] mri_surf2vol

Hello, I need to convert the white matte surface to a volume :binary volume with 1 in white matter and 0 outside. I am using the mri_surf2vol command (on both hemisphere), and fill it using matlab. Do you know if it is possible to obtain the volume from the surface already filled ? Thanks a lot

[Freesurfer] sphere registration

Hi I am using the freesurfer Parcellation, modify the obtained parcels to have a small rois. To validate my parcels subdivision into small rois, I need to know the variation of some roi_gravity_centers. Do you think that with the vertex number on the sphere of a subject (after parcellation) is it

[Freesurfer] analyze orientation

Hello, I have some analyze images (128*128*68), and I did not understand the way to read them correctly (with mri_convert). For the moment I am using : 'mri_convert chuv70 -it img -ot mgz 001.mgz'. This command works but gives me INFO: could not find .mat file for direction cosine info. In the

[Freesurfer] maximum number of ROI in atlas

Hello, I am modifying the 35-entries atlas by subdividing some parcels into N rois. Is there any limitation of the number of regions in an Atlas? Or an annotation file? Because when I have more than 300 region of interest in the atlas, the display of some region failed (gray) and the corresponding

RE: [Freesurfer] use modified annotation file for parcellation

skipped in mris_ca_label with my gcs file? And why there are '0 changed' in gibbs step? Thank you very much for your help -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: lundi, 5. mars 2007 21:22 To: Leila BH Cc: freesurfer@nmr.mgh.harvard.e

[Freesurfer] remote access

Hello, I tried to do remote access from my windows xp computer to the linux one, I follows the steps described in the freesurfer web pages. The remote access seems work correctly, but when I try to run freesurfer (tksurfer) it does not work, this is the error: Someone can help me?? I already ins

[Freesurfer] use modified annotation file for parcellation

Hello, I modified the annotation file rh.aparc.annot to 'rh.myaparc.annot' I can read it with read_annotation.m and it seems correct. (The modification is simply a subdivision of the middletemporal to 32 subregion named : middletemporal_1 .middletemporal_32). I copied this 'rh.myaparc.annot' f

[Freesurfer] output orientation incorrect

Hello, I am new freesurfer user, I need to have the labels of parcellation on analyze format. I did recon all command on my subject, I see the very beautiful parcellation on freesurfer. After reading all the question/response on the freesurfer website, I write my own txt file describing the 35 lab