Re: [Freesurfer] quantifyHippocampalSubfields.sh fails in the current version of freesurfer-Darwin-snowleopard-i686-dev.tar.gz

Hi Carl, the use of quantifyHippocampalSubfields.sh is: quantifyHippocampalSubfields.sh suffix outputFile [subjectsDirectory] Simply run quantifyHippocampalSubfields.sh T1 test_no-T1.txt or quantifyHippocampalSubfields.sh T1 test_no-T1.txt /Applications/freesurfer/subjects/RBrain and

[Freesurfer] About zgees function missing link

Hi, I was trying to compile freesurfer on an arm machine and I worked my way through quite a few obstacles. But when I am compiling the package mri_robust_register, I came across an error which stated that there is a function zgees_(*) in MyMatrix.cpp being undeclared. I wonder if anyone knows

Re: [Freesurfer] bad magic number

Hi Matthew, Thanks for getting back at this. We only process data for our users, so I don't have permission to share a sample with you. But I'll ask around to see if I can get a scan for you. To be honest, we aren't quite sure if the problem is with nibabel (v1.3.0). I tried to reproduce the

[Freesurfer] orientation flipped after mri_label2vol

Hi Freesurfer, We've carried out the mri_label2vol step for ROIs in one hemisphere. When opening in ITKsnap the orientations appeared flipped, with the axial ROIs overlayed onto the coronal orientation, and coronal over the axial, and the sagittal plane appeared rotated. Can anyone help us fix

Re: [Freesurfer] FS-FAST bbr registration

No, sorry. You can run tkregister-sess and it will show each one sequentially. This is a good idea and it may be possible with the transition to freeview. doug On 6/10/15 7:16 PM, sabin khadka wrote: Hi all- Is there a command we can have screenshots (similar to one employed in fsl) of

Re: [Freesurfer] orientation flipped after mri_label2vol

Hi Stefani are the axes also flipped if you view in freeview? cheers Bruce On Thu, 11 Jun 2015, Stefani O'Donoghue wrote: Hi Freesurfer, We've carried out the mri_label2vol step for ROIs in one hemisphere. When opening in ITKsnap the orientations appeared flipped, with the axial ROIs

Re: [Freesurfer] Read .mgz file matlab

and can you load the same volume into freeview? On Wed, 10 Jun 2015, dgw wrote: What command did you type? On Wed, Jun 10, 2015 at 5:32 PM, Mohammed Goryawala mgory...@fiu.edu wrote: Hello All, I am trying to read .mgz files into matlab on MacOSX using the MRIread command. It returns

Re: [Freesurfer] selx3avg-sess and monkey data

The easy fix is to edit rawfunc2surf-sess and remove the --cortex flag. Alternatively, you could run mri_vol2surf yourself from a script that you write. I've fixed this in version 6 to allow turning off the use of --cortex. doug On 06/09/2015 05:53 PM, Jackie Lam wrote: Hi all, I’ve

[Freesurfer] preproc-sess creates files

Hello Freesurfer team When I ran preprc-sess of dementia patient's fmri, fmcpr.nii. files and register.dof6.dat were not created automatically after preproc-sess. Thus I had to bbregister in two dementia patients manually. However recently I did preproc-sess in the another patient, fmcpr.nii

[Freesurfer] Research Assistant Job, Chicago, IL

Research Study Assistant job available at Northwestern University’s Cognitive Neurology and Alzheimer’s Disease Center in Chicago, IL. The research assistant will be responsible for analysis of neuroimaging datasets, in order to contribute to neuroscientific studies of normal aging and

[Freesurfer] working on different workstations

Dear Freesurfer team, I had read a paper a while ago (see attached) on the effects of changing workstation type across data. I was wondering if that is still an issue. I have a situation where a set of data were processed on a Mac with this version of freesurfer:

[Freesurfer] WM Edits not updating in batch

Hello Freesurfer Experts, I'm trying to troubleshoot a problem where the main surface in our brains is not adjusting following white matter edits using Freesurfer 5.3. To be clear, the procedure here is: 1) Make edits to wm.mgz 2) Run recon-all -3T -mprage -autorecon2-wm -autorecon3 Following

Re: [Freesurfer] WM Edits not updating in batch

Hi Kate, I am having trouble viewing the image. Could you send it as an attachment? When you say main surface, are you referring to the pial or white surface? -Allison On 06/11/2015 03:07 PM, McLaughlin, Katie wrote: Hello Freesurfer Experts, I'm trying to troubleshoot a problem where the

[Freesurfer] sagittal slices

I used the following command to convert a sagittal slice from analyze to mgz format. The original was acquired in an anterior to posterior/right to left angle of slices. However, while it is converting to an mgz properly, it seems to be giving me a flip upside down, and reverting to transverse

[Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04

Hi, Is there any plan by the Freesurfer team to address this well-known bug? http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35938.html http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36193.html For now the only workaround is to enter values through

Re: [Freesurfer] preproc-sess creates files

I'll need more information before I can help you. Please review our bug reporting page to see what kind of info is needed: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting On 06/11/2015 02:44 PM, Park, Jung Mi wrote: Hello Freesurfer team When I ran preprc-sess of dementia patient's fmri,

Re: [Freesurfer] sagittal slices

Do you not have the image in something other than analyze? If not, then just keep playing with the letters (ie, PIR) until you get it right. Note that you will not know what is left and right unless you have a fiducial on the subject doug On 06/11/2015 04:19 PM, Kriegel, Jennifer Lynn Sarai

[Freesurfer] Longitudinal Freesurfer | BA labels does not change

Hello All, I ran the freesurfer longitudinal stream for a subject with three time points and found that the /stats/lh.BA.stats has remained constant across all time points where as aseg.stats showed variations. Sorry if this question is too nieve. Thanks, Pradeep

Re: [Freesurfer] Inquiry about error message when run 'Tracula'

Hi Anastasia, Yes. I tried to run bedpostx on a stand-alone computer but it is very slow although it can work well. Regarding the b-values, we do have some subjects which were scanned in different protocols a few years ago. If it is possible, please add the option to the new version of

Re: [Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04

Hi Reza can you use freeview for what you want instead? tksurfer and tkmedit are deprecated cheers Bruce On Thu, 11 Jun 2015, Reza Rajimehr wrote: Hi, Is there any plan by the Freesurfer team to address this well-known bug?