[Freesurfer] GCA file

possible to do it ? Regards, Sophie Maingault – Doctorante/PhD student GIN (Groupe d'Imagerie Neurofonctionnelle) UMR 5296 – Université de Bordeaux – CNRS/CEA 146, rue Léo Saignat – Case 71 33076 Bordeaux cedex ___ Freesurfer mailing list Frees

[Freesurfer] Access the CVS source-code

(/usr/fscvsroot/dev/#cvs.lock): Permission denied cvs checkout: failed to obtain history lock in repository `/usr/fscvsroot/dev' cvs [checkout aborted]: read lock failed - giving up If anyone knows how to fix it ? Thanks by advance! Sophie Maingault – Doctorante/PhD student GIN (Groupe d&#x

Re: [Freesurfer] Access the CVS source-code

Hello, I tried this morning and it didn't work. Did you know if the issues with the server are resolved ? Sophie Maingault – Doctorante/PhD student GIN (Groupe d'Imagerie Neurofonctionnelle) UMR 5296 – Université de Bordeaux – CNRS/CEA 146, rue Léo Saignat – Case 71 33076 Bordeaux c

[Freesurfer] Error with bbregister (using T2 to refine pial surface)

Dear FS experts, I'm trying to use T2 weighted image to refine the pail surface. I have this error message : ERROR: you must have the FSLDIR environment variable defined and pointing to the FSL installation In release notes, I saw that in "known issues" : fslregister (and so bbregister with --in

Re: [Freesurfer] Comparison between fsaverage and a template created from scratch

Maingault Cc : "freesurfer@nmr.mgh.harvard.edu" Objet : Re: [Freesurfer] Comparison between fsaverage and a template created from scratch Hi Sophie I think fsaverage was made from 40 subjects so your 80 subject average will naturally be smoother Cheers Bruce On Oct 11, 2013, at 11:35

[Freesurfer] pial_lgi in QDEC

Best regards. Sophie Maingault ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe

[Freesurfer] Problem with the Monte Carlo simulation

bject ". Thus I have two questions: 1) is it possible to adapt the Monte Carlo simulation to our template using some command line or something else? 2) If not what advice can you give to us? Thanks a lot, Best regards, Sophie Maingault ___ Freesurf

[Freesurfer] Per-vertex regression model

--pvr » for per-vertex regressors? Is that possible or not ? If yes could i have some extra information to use properly the command ? Thanks by advance, My best, Sophie Maingault - PhD Student IMN, Institut des Maladies Neurodégénératives, UMR 5293 Equipe 5 : GIN, Groupe d’Imagerie Neurofonction

[Freesurfer] Comparison of the slope of the pvr analysis between groups

Dear FS experts, There is already a post about that but the concerned person never answered so there is no solution. I’m currently running per-vertex analyses with the --pvr flag of mri_glmfit command. I did correlations between 2 vertex-wise variables correcting for age. I also would like to

[Freesurfer] Template from scratch

Hi Experts, I'm creating a template from scratch. When I run mris_make_template is it enough to run mris_make_template ?h smoothwm my.temp0.tif ? My question is about which sphere_name I have to put for argument ? I hope I was clear. Best regards. Sophie __

Re: [Freesurfer] Template from scratch

9, « Douglas N Greve » a écrit : >I'd suggest running make_average_subject which will create tiffs for you >as well as other useful template-specific maps (like an annotation). >doug > >On 04/17/2013 05:48 AM, Sophie Maingault wrote: >> Hi Experts, >> >> I'

[Freesurfer] mri_glmfit-sim - error of fwhm

Dear experts, I have a error message when I use the command : mdi_glmfit-sim ‹glmdir X ‹cwpvalthresh 0,001 ‹cache 3 abs ERROR : cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage_sym/lh/cortex/fwhm00/a bs/th20/mc-z.csd I don't understand why because to create this glmdir I use a

[Freesurfer] What is "CSF" label is aseg.stats

Dear all, I read the others posts about CSF but I didn't find the information that I need. I would like to calculate total CSF and in the aseg.stats file there are : Lateral-Ventricle, Inf-Lat-Vent, 3rd Ventricle, 4th Ventricle, 5th Ventricle but what is CSF ? Because I read that freesurfer can

[Freesurfer] qdec and file "-qcache"

Hello everyone ! I want to use qdec so I tried to smooth the subjects with the following command: recon-all -s < t0001 . t0742 > -qcache (. = all my subjects !). The tutorial said that it takes about an hour but immediately a file was created : "-qcache" (2.95 Ko). Is it normal ? Does the proce

[Freesurfer] Recon-all with my own template

Hello Freesurfer experts ! I created a new template with make_average_subject called 80tvs and I would like to re-run some of my subjects with this new template. I can't find the command line in FAQ. Is it for example : recon-all -all -s t0001 -target 80tvs ?? So I need the repertory of this ne

[Freesurfer] Change of thickness with age with tksurfer

Hello, I used qdec to visualize correlation between cortical thickness and age. With tksurfer, when I load the file sig.mgh I can see the p-value for each vertex (log10 pvalue) but I would like to load a file which show the value of the slope, I mean the change of thickness with age. Which file

[Freesurfer] Cortical thickness asymmetries ?

Dear experts, I would like to study cortical thickness asymmetries. According to old messages it seems impossible so I would like to know if it is always the case or not ? Maybe, there is a command to subtract the values for each vertex in the left hemisphere minus the values for each vertex in

[Freesurfer] Asymmetries of cortical thickness

Hello, I obtained a map of cortical thickness asymmetries after the registration on the symmetric atlas. But I would to obtain the same map with raw data I mean just by subtract lh.thickness and rh.thickness. How can I modify the part #Create a stack of subjects in wiki page ? I have to registe

[Freesurfer] mri_surfcluster and "sub-clustering"

parate one apparent cluster in several sub clusters by extracting several maximum vertices and not only one per cluster ? Best, Sophie Maingault – Doctorante/PhD student GIN (Groupe d'Imagerie Neurofonctionnelle) UMR 5296 – Université de Bordeaux – CNRS/CEA 146, rue Léo Saignat – Case 71 33076