Re: [Freesurfer] Repeated amygdala dev7-segmentation volumes do not correspond

Dear Reetta-Liina, Is this on the same machine, platform, etc? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 08/11/2017, 20:45, "freesurfer-boun...@nmr.mgh.har

[Freesurfer] Where is the result of mris_pmake ?

Dear surfers, I am trying to measure the distance between two activated vertices... Now, I run "mris_pmake --optionsFile=options.txt" and here is the options.txt file below , But I did not get any result on the window or ./ores.log file... How can I get the result from mris_pmake ?

Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

Thanks you for your reply. I have used surfreg script and now it runs correctly. However, my subject list is very long, I have 100 subjects and running surfreg with all subject takes 13 hours (using all my cpus in a parallel way). Is there any option to reduce this long time? Any cuda file? T

Re: [Freesurfer] Repeated amygdala dev7-segmentation volumes do not correspond

Yes, all the specs are absolutely the same, same machine, same platform etc. No parallelization. Thank you for the help! Best, Reetta-Liina Lähettäjä: freesurfer-boun...@nmr.mgh.harvard.edu käyttäjän puolestaIglesias Gonzalez, Eugenio Lähetetty: 9.

Re: [Freesurfer] Repeated amygdala dev7-segmentation volumes do not correspond

Dear Reetta-Liina, After discussion with Koen Van Leemput, I believe I know what the source for these differences it, and it should be fixed soon. Having said that, I wouldn’t worry too much about a 2 cubic mm difference between two runs. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior R

Re: [Freesurfer] Local gyrification index - vertex-wise analysis values

Don't know what you mean by "extract lGI values from surface data" if not using mri_segstats as we've discussed. I think you can do the comparison you want  in the GLM using a "two group" analysis where one group only has one subject. On 11/09/2017 01:46 AM, Buse Merve Ürgen wrote: > Thank you

Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

no, sorry On 11/09/2017 03:50 AM, M del Mar Velasco wrote: > > Thanks you for your reply. > > I have used surfreg script and now it runs correctly. However, my > subject list is very long, I have 100 subjects and running surfreg > with all subject takes 13 hours (using all my cpus in a parallel

Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

It might capture specific anatomical features that are unique to your data set. It can be tricky though as you need to make sure to include an equal mix of all your groups. Eg, if you have 20 ADs and 10 controls, you'd need to make an atlas with 10 ADs and 10 controls. On 11/08/2017 03:57 PM,

Re: [Freesurfer] Creating cached versions of Xhemi registrations

Sorry, caching is not possible with xhemi. You can just run the mris_preproc command multiple times, one for each subject, specifing a subject-specific output file for each. This is all  that the -qcache flag does anyway On 11/08/2017 02:10 PM, Mehta, Chintan wrote: > > Dear FreeSurfer Users,

Re: [Freesurfer] preproc-sess with symbolic links

Why do you think this has to do with sym links? Can you run the preproc-sess command with -debug as the first option and send the results? On 11/08/2017 11:50 AM, Tuominen, Lauri Johannes wrote: > Hi all, > I’m trying to run preproc-sess using symbolic links in my SUBJECTS_DIR but > the program

[Freesurfer] Creating functional ROI

Dear FreeSurfer community, I am new to FreeSurfer and I apologize in advance if my questions are too naiive. I have some nii files for both a localizer and an experiment. I would like to find some ROIs in the localizer, get their coordinates, create a mask, and then find those regions on the expe

Re: [Freesurfer] longitudinal base error. (not a netCDF file)

Hi Paul, you can try to re-run from scratch (ensure there is enough space on the disk) and if you can replicate the problem start dropping some of the flags (like the parallel and the bigventricles etc, to find out if this is caused by one of the flags.) Anyway it looks more like an IO proble

Re: [Freesurfer] longitudinal base error. (not a netCDF file)

Hello Martin, I tried your first suggestion (removing the flags) and I got the same errors. Yes, I do have enough space on the disk and nu1.mnc file does exist. Do you think my script is the problem? I have attached the new recon log file and my script. Thanks. Best, Paul On Thu, Nov 9, 2017 at

Re: [Freesurfer] Creating cached versions of Xhemi registrations

Dear Doug, I think that is essentially what I figured. Based on remarks in other posts, my steps for evaluating laterality index entail applying: (1). Apply mri_preproc for each subject $SUB and $meas (area or thickness) individually using -xhemi flag but without any paired differences via: >

Re: [Freesurfer] surface based fMRI gorup analysis from spm

Thank you very much for your help, that almost fixed the problem.. Indeed it seems like it worked well for the first subject, but then it crashed for the second one.. this is the last part of what it typed on the command window: % Cleaning up --- rm -r ./tmp

Re: [Freesurfer] QDEC

Hi Doug, do you have any other ideas why I can´t open the project file? Best, Philipp Von: im Auftrag von "Kinzel, Phillipp" Antworten an: Freesurfer support list Datum: Mittwoch, 8. November 2017 um 14:33 An: Freesurfer support list Betreff: Re: [Freesurfer] QDEC Hi Douglas, thank you for

Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

Thank you for the insight; that is very interesting. I'm performing tests of continuous independent variables over a single sample of normally developing children (ages uniformly distributed from

[Freesurfer] Getting aparc.a2009s.annot in MNI

Hi All, I processed a bunch of subjects using recon-all, but now I would like to get labels from aparc.a2009s.annot from each subject in MNI space in nii from, the problem is that the annotation file (lh and rh) is in subject native space. I have a grey matter mask in MNI from each subject and my

Re: [Freesurfer] Getting aparc.a2009s.annot in MNI

Hi Daiana You should be able to use mri_vol2vol on the aparc+aseg.mgz and the talairach.xfm in the subject's mri/transforms dir. cheers Bruce On Thu, 9 Nov 2017, Daya P wrote: > Hi All, > I processed a bunch of subjects using recon-all, but now I would like to get > labels from > aparc.a2009s

[Freesurfer] comparing sphere and sphere.reg

Hi, I'm trying evaluating the distortion for each subject from their native space to fsaverage atlas space. Is it a appropriate measure to compare ?h.sphere and ?h.sphere.reg? I assume that by comparison, I may get the how each vertex warped during the registration? Thanks! Best, Tony

Re: [Freesurfer] comparing sphere and sphere.reg

Hi Tony you can do that but it won't measure the distortion induced by the sphere mapping itself. cheers Bruce On Thu, 9 Nov 2017, tony han wrote: Hi, I'm trying evaluating the distortion for each subject from their native space to fsaverage atlas space. Is it a appropriate measure to c

Re: [Freesurfer] Getting aparc.a2009s.annot in MNI

Hi Bruce, Can you give me some example code? I am not sure where the talairach would go? On Thu, Nov 9, 2017 at 1:21 PM, Bruce Fischl wrote: > Hi Daiana > > You should be able to use mri_vol2vol on the aparc+aseg.mgz and the > talairach.xfm in the subject's mri/transforms dir. > > cheers > Bru

Re: [Freesurfer] Getting aparc.a2009s.annot in MNI

Hi Daiana run mri_vol2vol --help. It has a bunch of examples and quite extensive help (thank you Doug!) Bruce On Thu, 9 Nov 2017, Daya P wrote: > Hi Bruce, > Can you give me some example code? I am not sure where the talairach would go? > > > On Thu, Nov 9, 2017 at 1:21 PM, Bruce Fischl > w

[Freesurfer] localGI issues

Hello experts, I am using FreeSurfer version 6 and am trying to run recon-all -localGI. Each time I run it, it fails on make_roi_paths. Below is an excerpt of the recon-all.log file. Any help is much appreciated. #@# Local Gyrification Index lh Thu Nov 9 14:06:42 PST 2017 mris_compute_lgi

Re: [Freesurfer] hemisphere analysis

Dr. Douglas, I try #3 method, when I run mri_glmfit, get error. The code I used: [mtobia@localhost lh.lh-rh.thickness]$ mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh Reading source surface /HD4/subjects_results_symptom//fsaverage_sym