Re: [Freesurfer] Error in Monte Carlo simulation

Thanks very much for your reply. I'll try de command-line programs then. Best regards, Ph. -Message d'origine- De : freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] De la part de Douglas N Greve Envoyé : mercredi 14 octobre 2015 21:56 À :

[Freesurfer] malloc error with mri_glmfit-sim

Dear FreeSurfer experts We are getting a malloc error in mri_segstats when trying to run mri_glmfit_sim (v5.3.0 on Ubuntu) as follows: mri_glmfit-sim --glmdir lh.pial_lgi.glmdir --cache 1.3 abs --cwpvalthresh 0.05 --overwrite The output ends with: Reporting on 2 segmentations Computing spatial

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

Thank you Martin.I am trying to run the following command line and get the error below. Would you have a suggestion to overcome this issue?Just in case I am also including a snapshot of my loaded variables at the bottom.Many thanks,Pablo>> lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);

Re: [Freesurfer] Extracting individual vertex values for surfaces mapped to fsaverage

Hi Bronwyn the lh.thickness.fwhm10.fsaverage.mgh has been mapped to fsaverage, so you need to read in the fsaverage parcellations. cheers Bruce On Thu, 15 Oct 2015, Bronwyn Overs wrote: > Hi Bruce, > > Following up on your comment below, if I am using > 'lh.thickness.fwhm10.fsaverage.mgh'

[Freesurfer] Error during long_mris_slopes

Dear FreeSurfer Experts While performing the long_mris_slopes --qdec I receive the following error: Traceback (most recent call last): File "/Applications/freesurfer/bin/long_mris_slopes", line 1125, in shutil.rmtree(dirname) File

[Freesurfer] Error during long_mris_slopes

Dear FreeSurfer Experts While performing the long_mris_slopes --qdec I receive the following error: Traceback (most recent call last): File "/Applications/freesurfer/bin/long_mris_slopes", line 1125, in shutil.rmtree(dirname) File

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

Hi Pablo, looks like on your system only 4 parallel workers are allowed, while the code asks for 8. Probably there is an easy way to specify that it should only use 4. Maybe Jorge or someone else who knows parallel matlab programming can answer. Best, Martin On 10/15/2015 07:18 AM, pablo

[Freesurfer] Tracula stats COR-.info does not exist

Dear Tracula developers I thought I had nearly reached the end of tracula processing. However, when I perform the step, trac-all -stat -c dmrirc_ind_mni_cvs_all_stats.all I receive this error message . Base name of output files:

Re: [Freesurfer] Error during long_mris_slopes

Hi Benedikt, hmm, strange. The rmtree command should delete the temp directory with everything in it. Are there any read only files in the directory? If it is empty check for hidden files (starting with a . )? Could also be a race condition, that some temp file is still being created while it

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

Hi Pablo The error you are getting is because in your Matlab setup you can only request a maximum of 4 matlab parallel workers and by default lme requests 8. So you just need to modify your command like this: lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex, [], 4); Please make sure that

[Freesurfer] Compiling dev version in ubuntu 15.10

I'm preparing to migrate over to the new Ubuntu when it comes out. I'm having the following issues compiling it: The included VXL library doesnt compile, using the system version seems to fix this: /usr/pubsw/packages/vxl/current/include/vxl/core/vnl/algo/vnl_symmetric_eigensystem.h:82:1:

[Freesurfer] editsFail

Hello, I am using free surfer version 5.0.0; how do I continue to edit the brain with the previous edits made if the brain was processed under applyEdits, but is now in editsFail? Does this mean that I have to redo the entire brain, or can I have it restored somehow? Thank you Timothy Le

[Freesurfer] FreeSurfer and OpenMP

I would like to use freesurfer with OpenMP, with 4 processors. I wrote this : recon-all -all -i /mnt/linuxwin/lboumgha/data/CENTER_TBI/tro/suj1/T1.nii.gz -subjid subj1 -openmp <8> and I got this error message : bash: syntax error near unexpected token `8' What is the good syntax if I want tu

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

Thanks you for the replies.Jorge and FS experts,I have run the analysis and first double checked that the sum of vectors of (ni) is equal to the number of rows in (X). Both are 140 which is the number of my subjects.The analysis gave the following 'error'(?) below:I looked up a previous thread

Re: [Freesurfer] error using mri_glmfit

Hi Doug, Thanks. Please see attached for the files in their original format. I realized the GLM for model 1 (discrete factors for maltx, parent ed and sex, continuous: age) might be failing bc one of the 8 groups (2maltreated*2parented*2sex) has only 1 subject. My apologies for my delayed

[Freesurfer] Make average subject from additional data

I have a group of subjects that I have run through the standard freesurfer (version 5.3) pipeline, for the same subjects I also have T2 volumetric data and I have created T1/T2 ratio images for each subject. I have registered the ratio images into Freesurfer space and used mri_vol2surf to

Re: [Freesurfer] error using mri_glmfit

yes, you have to have more than 1 subject in the group if you are going to use DODS. It should work with DOSS, though you probably don't want to do tests with that "group" On 10/15/2015 01:15 PM, Gold, Andrea (NIH/NIMH) [F] wrote: > Hi Doug, > > Thanks. Please see attached for the files in