Re: [Freesurfer] control points

Hi Bruce, Sorry for the multitude emails. I have attempted to upload via both FTP and Martinos file drop. The martinos site keeps dropping out, and FTP is giving the following error: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp> cd transfer/incoming

[Freesurfer] Pial extension into cerebellum

Dear Freesurfer Experts, I have read the advice on the wiki regarding what to do when pial surfaces extend into the cerebellum. I had a few questions to clairfy things: 1) If I have made other (non-cerebellar) edits to the brainmask.mgz, and added control points can I simply do cp brainmask.mgz

Re: [Freesurfer] FSFAST v 5.1 group level volume analysis

Hi Tapsya, try adding "-no-subcort-mask" to your mkanalysis-sess command line. doug tap...@nmr.mgh.harvard.edu wrote: > Hi Doug, > > http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes states that "FSFAST > - now masks the volume-based analysis to include only subcortical areas" > and indeed, i

[Freesurfer] FSFAST v 5.1 group level volume analysis

Hi Doug, http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes states that "FSFAST - now masks the volume-based analysis to include only subcortical areas" and indeed, it looks like our group level volume results are in subcortical space only. We always use volume (native space full brain) analys

[Freesurfer] how to convert the *.annot to *.gii

Hi, dear experts, In freesurfer , is there a way to convert the" *h.aparc.annot" file to Gifti file format so that caret can recognize it. thanks yuning ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailma

[Freesurfer] bug in FS permutation

Hi Y'all, I have just found a bug in our implementation of the permutation test. It does not affect all permutations, so read on to figure out if it affects you. The bug is that the histogram that is created by the permutation simulation is always based on the last contrast in the analysis. The

Re: [Freesurfer] overlay alignment in tkmedit

Hi Anthony, there's something I don't understand here. You said that ahuman_1_do_shft.nii was used as input to to create chuman_1_do_shft.nii, but they have different sizes, so something else is happening along the way, and this is causing the problem. One thing you can try first is to load

Re: [Freesurfer] mri_convert question

Are you using the same viewer? On Tue, Jan 17, 2012 at 11:34 AM, Antonella Kis wrote: > Dear all, > > I wonder why when I am using the mri_convert to convert my mgz image which > is very little tilted to the left into a nii.gz image which  appears very > little tilted to the right instead to keep

[Freesurfer] mri_convert question

Dear all, I wonder why when I am using the mri_convert to convert my mgz image which is very little tilted to the left into a nii.gz image which  appears very little tilted to the right instead to keep the same  direction to the left. I was using: mri_convert /media/2Tra/Antonella_2011/DTI_F

Re: [Freesurfer] Converting mgz to nii.gz

Hi Antonella, If you are applying the morph to a mask file, then yes, the nearest neighbor interpolation shoudl be used. The masking option that you ask about below depends on whether you want to use wmparc to guide your masking (option 1) or whether you want to do the masking based upon in

Re: [Freesurfer] Newbie question: mean/stddev for volumes and thicknesses in an atlas

Hi Bruce, I had a feeling you were going to say that I needed to be careful about scanners and sequence parameters :-) The Oasis dataset looks like just what I would need to get a sense of things, as you said. What should I do to get the segmentations? Cheers, Souheil On Jan 17, 2012, at 8:4

Re: [Freesurfer] Newbie question: mean/stddev for volumes and thicknesses in an atlas

Hi Souheil, the problem is that you'll really want to match acquisition parameters as well as several demographics (e.g. age, gender, etc, SES, ...). If you just want to get some feeling you could try looking at the Oasis dataset, for which we have segmentations, or you could post your sequence

[Freesurfer] update version of tksurfer and freeview

Hi When I was at the Freesurfer course in December we used an updated version if Tksurfer and Freeview. Is it possible to get a download link to thesse new version of Tksurfer and Freeview please? Cheers Knut J _

Re: [Freesurfer] Newbie question: mean/stddev for volumes and thicknesses in an atlas

Hi I use this script to extract mean cortical thickness. The script is available under GNU GPL3. Knut J Bjuland > From: souheil.in...@nih.gov > To: freesurfer@nmr.mgh.harvard.edu > Date: Mon, 16 Jan 2012 23:04:09 -0500 > Subject: [Freesurfer] Newbie question: mean/stddev for volumes and

[Freesurfer] Postdoc position in neuroanatomical MRI of developmental dyslexia

Applications are invited for a postdoc position in the team of Franck Ramus, LSCP, Institut d'Etudes Cognitives, Ecole Normale Supérieure, Paris, France. The successful candidate will investigate neuroanatomical differences between dyslexic and control children, using high-quality 3T MRI images f