Re: [Freesurfer] xhemi

When creating a laterality-free atlas one needs to make sure to do the same thing to the left and right hemi. Eg, the mni152 is not laterally symmetric, so you will get a different registration when you register your volume directly to the mni152 vs left-right reversing your volume and then reg

Re: [Freesurfer] ascii: bad interpreter: No such file or directory

External Email - Use Caution Thanks again Yujing. There is not, here is a screen shot of the command (I removed the other inputs for clarity) followed by the output, which is just "segmentation fault (core dumped)" [image: image.png] I think before you asked which free surfer ve

Re: [Freesurfer] ascii: bad interpreter: No such file or directory

It is hard to tell without the data. Is there any output before the core dump? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Sennott, Liam Ricker Sent: Wednesday, March 6, 2024 4:28 PM To: Freesurfer support list Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or dire

Re: [Freesurfer] ascii: bad interpreter: No such file or directory

Sending on behalf of Brian who was having trouble sending a reply: Dear Yujing, Thank you! Haha yes, a silly error there with the -1/-l. When I correctly put -l, I now get the following error: "segmentation fault core dumped". Might this error make any sense to you? Brian From: freesurfer-b

[Freesurfer] Hi

hfarza...@mgh.harvard.edu Get Outlook for iOS ___ 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

[Freesurfer] Spring 2024 FreeSurfer course

Hello all, The next virtual FreeSurfer course will be held on April 29th, 30th, and May 1st. Registration for this virtual FreeSurfer course is opening on Monday, March 11th at 12pm Eastern Daylight Time. Visit our course website to find out more information: https://surfer.nmr.mgh.harvard

Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area

Hi Taylor, Thanks for sharing the data. I see the problem now. The first 14336 bytes of your rh.area fit SIGNA_FILE criteria. So, it is read as SIGNA_FILE instead of MRI_CURV_FILE. We will have a fix in dev version. But I’m not sure how to get around this in FS 7.2. Best, Yujing From: free

Re: [Freesurfer] ascii: bad interpreter: No such file or directory

Sorry, just recognized it. The option to pass label file is ‘-l’. It looks like you have ‘-1’ instead. From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Huang, Yujing Sent: Wednesday, March 6, 2024 10:57 AM To: Freesurfer support list Subject: Re: [Freesurfer] ascii: bad interpreter:

Re: [Freesurfer] ascii: bad interpreter: No such file or directory

I’m not sure which version of Freesurfer you are using. But it seems the command line options are not in the right order. Here is the wiki help - https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Kavanaugh, Brian

Re: [Freesurfer] xhemi

External Email - Use Caution Dear Doug, Thanks. A regional Laterality Index can be calculated using XHEMI (as described on the wiki) but also in a different way, e.g. using the default FS output from ?h*.stats files and e.g. doing (LH-RH)/((LH+RH)/2) or some other formula. You onc

Re: [Freesurfer] remote access to freesurfer installation...

No, sorry. We do have FS containers that you could use on AWS On 3/6/2024 9:28 AM, Gonzalo Rojas Costa wrote: External Email - Use Caution Hi: Is there a freesurfer facility where an MRI study can be processed remotely?   Sincerely, Gonzalo Rojas Costa _

Re: [Freesurfer] Unexpected skull shape after wraped to MNI

Can you be more specific about what abnormality you are seeing? The Screenshot2 does not look so bad to me. I'm assuming that this is the talairach.xfm transform you are talking about? If so, that is hardly used in the stream (and certainly not for placing surfaces), so it is no surprise that t

Re: [Freesurfer] aparc & wm underestimation

This is difficult to debug remotely. The first thing to look at is the ?h.orig surface. Does that look more-or-less right? If not, then it means that the wm.mgz is wrong. If it does not look right, it means that the surface placement algorithm is pushing the surface into subcortical gray. One w

[Freesurfer] remote access to freesurfer installation...

External Email - Use Caution Hi: Is there a freesurfer facility where an MRI study can be processed remotely? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e

[Freesurfer] ascii: bad interpreter: No such file or directory

External Email - Use Caution Hello everyone, I am new to freesurfer so I apologize if this is a simple answer. i'm running mris_ca_label to get the BN atlas parcellation: mris_ca_label -1 /users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label

Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area

It doesn’t look like rh.area is recognized correctly. ‘mri_info rh.area’ should show it is a ‘curv’ file with nvertices x 1 x 1 dimensions. I’m not sure where exactly the area values are calculated. What happen if you re-run this step? mris_place_surface --area-map ../surf/rh.white ../surf/rh.ar