Re: [Freesurfer] [FreeSurfer] : Convert asl data from fsaverage (surface) to MNI305 (volume)

Hello Douglas, I have download the new version of mri_surf2vol you supplied me, and have copied it in the FS5.3 /bin installation files. But when I tried to launch with my precedent command lines, the error message appeared : *gdiagno = -1Using identity

Re: [Freesurfer] mri_watershed Error: indices out of bounds

Hello Edgar, Could you upload the whole subject folder? I could try to run it through recon all here and see if I can reproduce the error. It would also allow me to look through your log files to see if I can spot anything that could be causing this issue. You can use FileDrop2.0 if the

Re: [Freesurfer] [FreeSurfer] : Convert asl data from fsaverage (surface) to MNI305 (volume)

Hello Douglas, I have downloaded a new license and it successfully runs ! Best regards, Matthieu 2015-03-31 12:39 GMT+02:00 Matthieu Vanhoutte matthieuvanhou...@gmail.com: Hello Douglas, I have download the new version of mri_surf2vol you supplied me, and have copied it in the FS5.3 /bin

Re: [Freesurfer] White matter and pial surfaces not tracking sulcus

Hi all, Sorry for the repost, was just wondering whether someone might have some input regarding this issue. Thanks! Niels On Thu, Mar 26, 2015 at 12:10 PM, Niels Bergsland theni...@gmail.com wrote: Hi all, I have run into an issue that I am having trouble correcting.

[Freesurfer] isxconcat-sess problem

Hi list, I'm performing the FS-FAST analysis. Some months ago, I have already preformed this analysis on some subjects without problem. Now, I have added some subjects. When I rerun the analysis i have these error: for isxconcat-sess -sf sessidlist —analysis fc.lthalseed.surf.lh -contrast

Re: [Freesurfer] longitudinal

Martin, Thanks for the advice. I'll have a think about which approach to take. Regards, Kate On Wed, Apr 1, 2015 at 2:24 AM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Kate, first you can check (and fix) the surface in the base. They are mapped from there to the time points, so

[Freesurfer] TRACULA: drmirc parameteres with already processed and registered data

Hello, I am interested in using TRACULA for my data, but I have a few questions about modifying the dmrirc configuration file. I have already conducted eddycorrect, bet, and dtifit in FSL, registration of T1 and dti using ANTs, and I have also registered individual subject data to a template

Re: [Freesurfer] longitudinal

Hi Kate, first you can check (and fix) the surface in the base. They are mapped from there to the time points, so improving the base will have an effect on both time points. checking surface placement can only be done by opening the images and surfaces manually. If you want to avoid that,

Re: [Freesurfer] GLM_Fit Question

Thanks so much! That did the trick. Taylor Elrod ___ 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

Re: [Freesurfer] 'current' FSL

It may help to provide a bit more context e.g. the email/instructions you where you found the reference to 'current' fsl version? HTH, D On Tue, Mar 31, 2015 at 3:31 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Other than someone's recollection, there is probably no verifiable means for

Re: [Freesurfer] 'current' FSL

I think he's referring to the convention used in the various /usr/pubsw/packages libraries where current points to a version number. For example as of right now: /usr/pubsw/packages/fsl/current - 5.0.7 But there is no real way of knowing the destination of that symlink at May 1 2012. At least

Re: [Freesurfer] 'current' FSL

Other than someone's recollection, there is probably no verifiable means for determining this information. Sending an inquiry to Martinos Center Help Desk is your best bet. -Zeke On 03/31/2015 03:24 PM, Marco Loggia, PhD wrote: Hi all, If I wanted to find out what was the 'current' FSL

[Freesurfer] 'current' FSL

Hi all, If I wanted to find out what was the 'current' FSL version at the Martinos Center on May 1, 2012, how would i do it? Thanks! Marco __ Marco L. Loggia, PhD Assistant Professor of Radiology Harvard Medical School Massachusetts General Hospital 149

Re: [Freesurfer] Accounting for lesions misclassified as non-brain matter

From: jennifer.fer...@alumni.ubc.ca Sent: Tuesday, March 31, 2015 11:04 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Accounting for lesions misclassified as non-brain matter Hi there, I am having an issue with stroke lesions that border onto the cortex being

[Freesurfer] TRACULA NIFTI Images

Dear Colleagues, I'm having problem to process TRACULA. I already processed the T1 imagens (recon-all) but I can't go further with the DWI imagens. I think that the problem is my image type. I have 33 files (1 b0 and 32 different directions) and in the configuration file I pointed to the first