[Freesurfer] Postdoc opportunity (2 years), C-Lab, Krakow (Poland)

External Email - Use Caution Dear all we are hiring a postdoc with strong experience in MRI data acquisition and analysis to collaborate on a large-scale international project ( https://skuldnet.org/) aimed at exploring the neural architecture of consciousness. For more informatio

[Freesurfer] Anatomical cluster description table from mri_glmfit-sim?

External Email - Use Caution Dear FS experts, From an statistical map obtained by mri_glmfit-sim, say a cache.th13.abs.sig.masked.mgh map, I would like to list all the significant regions from all clusters in the following intuitive way, for instance: Supramarginal gyrus: X verti

[Freesurfer] Join the final round of the IronTract Challenge

Dear all - This is your chance to enter the final round of the IronTract Challenge. First, make sure to check out the results of round 1 of the challenge, along with other great work in the ISMRM Orientation Modelling & Fibre Tractography oral session, and join us for the Q&A: https://ww5.aievo

[Freesurfer] tksurfer - failed to calloc

Hi Surfers, I get the following error when I use tksurfer for one of our subjects: znzTAGskip: tag=1830834290, failed to calloc 1834378240 bytes! To clarify, this error is only limited to freesurfer version 6.0 and 7. But version 5.3 works fine with the same subject. Regards __

Re: [Freesurfer] tksurfer - failed to calloc

Sorry, I think I figured the issue out based on the previous conversations. Just for the record, I sourced freesurfer 5.3 and resaved orig.mgz for this subject using the following command: mri_convert mri.orig mri.orig Apparently it corrected the problem. Regards __

Re: [Freesurfer] error in longitudinal stream fs7.1 ERROR: Number of filenames for --iscalein should agree with number of init LTAs (--ixforms)! worked in fs6

External Email - Use Caution Thanks I found a new bug, mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz error: No such file or directory error: MRIvoxelToTalairachVoxel: unsupported slice direction 2^@ Knut Jørgen Bjuland On 21/07/2020 16:27, Douglas N. Greve wrote: Yep,

Re: [Freesurfer] Fwd: Cortical Parcellations in FreeDurger 7

External Email - Use Caution Hi Douglas, mri_segstats wouldn't generate binary ROI masks, so I tried using *mri_binarize* and *mri_extract_label* to produce masks for thalamic nuclei, but I run into the same problem of generating empty masks (these commands worked for other ROIs)

Re: [Freesurfer] Error in Trac-All Pre-Processing step

Hi Jocelyn - I'm having a hard time replicating this error. What version of FSL are you using? You can see this in the file $FSLDIR/etc/fslversion. Thanks! a.y From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Jocelyn Ra Sent: Wednesday, July 8, 2020

Re: [Freesurfer] Error in Trac-All Pre-Processing step

External Email - Use Caution Hi Anastasia, I'm using FSL 6! Hope this helps, Jocelyn On Thu, Jul 23, 2020 at 8:47 AM Yendiki, Anastasia wrote: > Hi Jocelyn - I'm having a hard time replicating this error. What version > of FSL are you using? You can see this in the file $FSLDI