[Freesurfer] ventricular CSF volumes

Dear Freesurfers, I am calculatig with ventricular volumes in aseg.stats. 1. According to the archives Mail calculation of ventricular CSF is is instructed differently: - Bruce Fischl 2007 to Jenifer: Add ventricular volumes including CSF (segid 24): Left Lateral Ventricle (segid 4) + Left Infer

[Freesurfer] mris_label2annot & CLUT error

Hi all, I am trying to make a custom annotation file. In doing so, I have created a custom color lookup table. I have attached the CLUT. I run the following command: >> mris_label2annot --subject $SUBJ --hemi $HEMI --ctab $CTAB --a $OUT --l label_1 --l label_2 ... --l label_n And I receive the f

Re: [Freesurfer] Fwd: Problem running Tracula

This error means that the number of volumes in your diffusion data set doesn't match the number of lines in the bvecs/bvals files. You can run "mri_info dmri/dwi.nii.gz" to see the number of volumes in your data set. On Wed, 9 Sep 2015, andrea cristina Lima wrote: Dear Anastasia, I checke

Re: [Freesurfer] Segmentation in dev version

Correction in the previous message: I need to mask the functional images (EPI) for further analysis. On Wed, Sep 9, 2015 at 11:56 PM, Priyanka Mehta wrote: > Thank you for the explanation Lee. > I need to use the cortical labels for masking the T1 for further analysis. > Which file should I be u

Re: [Freesurfer] Segmentation in dev version

Thank you for the explanation Lee. I need to use the cortical labels for masking the T1 for further analysis. Which file should I be using then - wmparc.mgz or aparc+aseg.mgz? For the perirhinal cortex, I do not have the following files even after running recon-all /label/lh.BA.annot /label/rh.BA.

Re: [Freesurfer] Freesurfer Digest, Vol 139, Issue 14

ant Professor Department of Psychiatry and Behavioural Neurosciences DeGroote School of Medicine McMaster University Peter Boris Centre for Addictions Research 100 West 5th Street Hamilton, Ontario L8N 3K7 Canada Telephone: (+1) 905-522-1155, ext. 39014 Email: amlu...@mcmaster.ca Web

[Freesurfer] mri_deface questions

Hi all, I am working on defacing around 70 scans, and was using the mri_deface program to do so. To start off with, I ran them using the version of mri_deface from version 5.3, along with the .gca files included here: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface When I ran that, many of t

Re: [Freesurfer] Freesurfer Digest, Vol 139, Issue 14

r, so this may be a novice question. We are running recon-all and the script finished without errors for all of our subjects except for one. I have opened the recon-all.log file to examine the output, but am not sure where to locate the error. The last thing printed to the terminal window was a

Re: [Freesurfer] TrackVis Transforms

Hi Thomas - If you have a .mat transform, try dmri_trk2trk to apply it to a .trk file. You have to specify reference volumes for the input and output space. Best, a.y On Wed, 9 Sep 2015, Thomas Potrusil wrote: Dear FreeSurfers !! I´m trying to bring a trackvis .trk file to freesurfer space

[Freesurfer] Freesurfer/Qdec brain images

Dear Experts, I need some help regarding saving the brain images in Freesurfer/Qdec please: 1) Can I save the brain regions shown in Qdec group analysis as other files and view them in MRIcroN etc or does it only allow us to save the images as tiff files (inflated medial, inflated lateral, pial

[Freesurfer] TrackVis Transforms

Dear FreeSurfers !! I´m trying to bring a trackvis .trk file to freesurfer space but fail completely... I tried to execute the code descibed on the following page: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms and also read the detailes regarding trk-(header)-data descr

Re: [Freesurfer] Help with recon-all

Hi Michael sure, send us the recon-all.log. We don't get many segfaults, and usually they are because you ran out of RAM or disk space. Were you running other things on the machine at the same time? We will need this info: https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting cheers Bruce

Re: [Freesurfer] mri_compute_volume_fractions not filling some sulci properly

p.s. you can try increasing the resolution of the intermediate volumes using the -r switch. The default is 0.5. Try 0.25 (although this will take 8 times the memory and time I think). Make sure to put the -r 0.25 before before the mandatory options. If this does make things look significantly b

[Freesurfer] Help with recon-all

Hi all, I am new to FreeSurfer, so this may be a novice question. We are running recon-all and the script finished without errors for all of our subjects except for one. I have opened the recon-all.log file to examine the output, but am not sure where to locate the error. The last thing printed

Re: [Freesurfer] mri_compute_volume_fractions not filling some sulci properly

Hi Sebastien it's pretty hard to tell what's going on from a couple of slices. What was the command line you used? If you upload the subject I'll take a look (I'll need the exact command lines you ran as well). cheers Bruce On Tue, 8 Sep 2015, Sebastien Proulx wrote: My images don’t se

[Freesurfer] Automaticky: Jan Sanda is out of the office (a vrátí se ne 13.9.2015)

Od st 9.9.2015 do ne 13.9.2015 jsem mimo kancelář. Poznámka: Toto je automatická odpověď na vaši zprávu "[Freesurfer] Functional connectivity with volume label" odeslanou dne 9.9.2015 0:42:09. Toto je jediné oznámení, které obdržíte v době nepřítomnosti této osoby.