Re: [Freesurfer] Missing Control Points and QATools

Hi Matt I'm sorry to hear it. I've never heard of anything of ours deleting the control.dat unless you run recon-all with the appropriate -clean switch. I don't know an easy way to recover them. Do you need them back? You could do something like copy the subject, run the intensity normalizatio

Re: [Freesurfer] Missing Control Points and QATools

External Email - Use Caution Hi all, Sorry for the bump but I wanted to take one more shot at this. We're making it back but we've lost many, many hours of editing work. Has anyone else had experiences with QAtools, or other FreeSurfer utilities, removing control point data, or dis

Re: [Freesurfer] tractstats2table - all tracts for multiple subjects

External Email - Use Caution Thx Anastasia. This the command I used and the error: [hellerml@login01 processed_data]$ tractstats2table --load-pathstats-from-file /scratch/jimalex/freesurfer6_0_chd_auck_6yr/processed_data/test.list --overall --tablefile test.table Parsing the .s

Re: [Freesurfer] dwi.ecclog file

Hi Loic - The command that computes the motion measures is dmri_motion, and it can take either the eddy_correct or eddy format as input. The former format contains affine registration matrices with respect to the reference frame (which usually is the first b=0). The latter format contains the s

[Freesurfer] dwi.ecclog file

Hello, I have several questions regarding the dwi.ecclog file data from Tracula, using the FreeSurfer version V6.0.0. 1) Does Tracula still use eddy_correct from FSL, or was it updated with the new eddy function from FSL? 2) Are the values for each slice of dwi.ecclog relative to the first sli

Re: [Freesurfer] tractstats2table - all tracts for multiple subjects

Hi Jim - You can use the --load-pathstats-from-file option, as in the tutorial, to pass a text file that contains the paths to all the stats files that you want to include in the table. These can be from multiple subjects and/or tracts. http://freesurfer.net/fswiki/FsTutorial/TraculaStatistics

[Freesurfer] tractstats2table - all tracts for multiple subjects

External Email - Use Caution Hi, For a group analysis, it possible to use 'tractstats2table' to generate a single table that contains all the tracts for multiple subjects? It's not intuitively obvious looking at the options with the 'tractstats2table' utility. Jim "The

Re: [Freesurfer] crypt_gkey = (null)

Hello Aaron, The build timestamp from the output below shows mri_convert is from 8/2014. When I look at the build timestamp on our stable 5.3 version of mri_convert I see it is from 5/2013. So the version that you listed is about 1 year newer than the 5.3 release I can see. It is possible th

Re: [Freesurfer] crypt_gkey = (null)

External Email - Use Caution I checked my system is not encrypted. I had someone else run the command on the same machine. It worked for them. So I changed my BASH environment to a default environment. I still get the same error. I tried this again but with a different FreeSurfer

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

External Email - Use Caution Thank you Eugenio, there were no error messages or any observations that may indicate the computing process experienced perturbations... Nikita On Jun 12, 2018, at 12:19, Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk>> wrote: Exte

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

External Email - Use Caution Uuuummm it seems it died unexpectedly, but there’s no error at the end of the log… are you sure that’s the complete file? If not: did you get any other message on the screen when you tried to run this? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Sen

Re: [Freesurfer] Extract the entorhinal cortex as a mask

I think you can use 1006 (left) and 2006 (right) cheers Bruce On Tue, 12 Jun 2018, Erik O'Hanlon wrote: >External Email - Use Caution > > Hi Bruce, > > > Thanks. So if I use the following command > > mri_extract_Label aparc+aseg.mgz 216 EC.mgz > > would that give me both L and right EC e

Re: [Freesurfer] crypt_gkey = (null)

Hello Aaron, You could check to see if the CentOS 7 system is using disk encryption, e.g., if the following command return 1, then it would mean encryption is in use (which can be an issue with FreeSurfer). $ cat /proc/sys/crypto/fips_enabled If it returns zero, it could be an issue with a sys

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

External Email - Use Caution My apologies. Here is the long-hippocampal-subfields-T1.log https://drive.google.com/open?id=1VIeYRRBT1fNOeucsYSW2R1792g7u5JBD On Jun 12, 2018, at 10:45, Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk>> wrote: External Email - Use

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

External Email - Use Caution Thanks, Nikita. Can you please send us the file long-hippocampal-subfields-T1.log, which you can find under the base subject, for one of the failing cases? Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Comput

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

External Email - Use Caution Hi Eugenio, Thank you very much for your prompt reply. I was trying to support the tread titled Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files We received results from the cross-sectional s

Re: [Freesurfer] Extract the entorhinal cortex as a mask

External Email - Use Caution Hi Bruce, Thanks. So if I use the following command mri_extract_Label aparc+aseg.mgz 216 EC.mgz would that give me both L and right EC extracted? is there any way to get the left and right separately? Thanks so much for the help cheers Erik

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

External Email - Use Caution Hi Nikita, Could you please be a bit more specific about your problem? What issue are you exactly referring to? Also, can you please send us the log file of the hippocampal subfields (rather than of recon-all)? Cheers, /Eugenio -- Juan Eugenio Iglesi

[Freesurfer] crypt_gkey = (null)

External Email - Use Caution I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3. When i get to the part where MRI_convert is creating the the orig001.mgz its gives me a segmentation fault. if i run this on a centos 6 system it works fine. below is the output of

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

External Email - Use Caution HI I would like to report to have the same issue. There were no errors in the log yet the majority of results missing right hemisphere. Attaching here the log file, or you can also access it via googledrive here: https://drive.google.com/open?id=13P

[Freesurfer] Difference between Freesurfer and Voxel Based Morphometry

External Email - Use Caution Hi Freesurfer developers, I´m starting in structural MRI analysis with Freesurfer and i would like to know what is the main difference between freesurfer and the voxel based morphometry approach. It is more appropiate to use a method for some specific

Re: [Freesurfer] Extract the entorhinal cortex as a mask

Hi Erik yes, you can apply mri_extract_label to the aparc+aseg.mgz to extract EC as a volume mask cheers Bruce On Tue, 12 Jun 2018, Erik O'Hanlon wrote: >External Email - Use Caution > > Hi FS experts , > > > I'd like to make masks for the entorhinal cortex to use for tractography. Can

[Freesurfer] Extract the entorhinal cortex as a mask

External Email - Use Caution Hi FS experts , I'd like to make masks for the entorhinal cortex to use for tractography. Can you advise what FS tool should be used? I've used the mri_extract_label for my hippocampal masks but not sure what files to use to extract EC ? I'm sure it