[Freesurfer] Using own parcellation atlas

Hi experts, I would like to use a different atlas other than the 'default' Freesurfer atlases, namely the Gordon Parcellation (surface based parcellation of 333 ROIs of the cortex) to segment my T1 datasets. So I can go on to use these segmentations for DTI connectome analysis using MRTrix

Re: [Freesurfer] R package for graph theory analysis of MRI data {Disarmed}

I apologize but the link to the Github page is: https://github.com/cwatson/brainGraph Chris On Tue, Apr 11, 2017 at 7:37 PM, Chris Watson wrote: > Dear Freesurfer users, (apologies for cross-post) > > I am pleased to announce the first major release of my R package >

[Freesurfer] R package for graph theory analysis of MRI data {Disarmed}

Dear Freesurfer users, (apologies for cross-post) I am pleased to announce the first major release of my R package "brainGraph" (v1.0.0), a collection of functions for performing graph theory analyses of brain MRI data. I chose R because it is free and is, in my opinion, the best choice for just

Re: [Freesurfer] mri_convert defaults to trilinear interpolation if "--like" option is used, regardless of "-rt nearest"

use mri_vol2vol where you can control the interp. Or, for a binary mask or segmentation, use mri_label2vol On 04/11/2017 03:20 PM, Harris Hoke wrote: > > I’m currently running freesurfer 6.0.0, and I’ve run into the same > problem described in this thread on the archives >

[Freesurfer] mri_convert defaults to trilinear interpolation if "--like" option is used, regardless of "-rt nearest"

I’m currently running freesurfer 6.0.0, and I’ve run into the same problem described in this thread on the archives . Does anyone know if a fix exists? I'm trying to move binary parcel files from the SPM default MNI152

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

oh, I think I see the problem now. The input is surface-based data, but you did not include a --surf subject hemi option, so it thinks that it is a volume. On 04/11/2017 12:58 PM, Clara Kühn wrote: > Hi Doug, > > attached you find the rmanova directory after I ran the mri_glmfit command. I >

Re: [Freesurfer] ERROR: nu_correct

What version of freesurfer are you using? My guess is 5.3 or earlier? With pre v6.0 versions of freesurfer, the Talairach transform step will fail at the mri_nu_correct.mni command on newer Linux distributions that come with perl version 5.22 (and higher) due to an incompatibility with the mni

Re: [Freesurfer] recon-all -parallel osx sierra

Hello Jan, Yes, unfortunately this is a known issue with the -parallel flag on sierra. To resolve the issue, source freesurfer and then type the following command to update your installation: sudo -E fs_update You should then get a new reconbatchjobs scripts and the -parallel flag should

Re: [Freesurfer] QDEC and ROI drawing

Ok. Thank you! 2017-04-11 13:56 GMT-04:00 Douglas N Greve : > No. qdec is not being developed any more, so don't expect it to change any > time soon > > > On 04/11/2017 01:14 PM, Arnaud Boré wrote: > >> Do you know somebody who can tell us if qdec should be fixed or if

Re: [Freesurfer] freesurfer 5.1

The current license is backwards compatible and should work. Can you send me a copy of your current license file TO MY DIRECT EMAIL ADDRESS and I will take a look? -Zeke On 04/11/2017 01:02 PM, Suchandra Thapa wrote: > Hi, > > I'm trying to support some users that want to use Freesurfer 5.1

Re: [Freesurfer] QDEC and ROI drawing

No. qdec is not being developed any more, so don't expect it to change any time soon On 04/11/2017 01:14 PM, Arnaud Boré wrote: > Do you know somebody who can tell us if qdec should be fixed or if > it's a normal behaviour ? > > 2017-04-11 12:39 GMT-04:00 Douglas N Greve

[Freesurfer] freesurfer 5.1

Hi, I'm trying to support some users that want to use Freesurfer 5.1 for their workflow. How do I get a license file for this version? A license for the current versions doesn't seem to work. Suchandra Suchandra Thapa sth...@ci.uchicago.edu Computation Institute Searle Chemistry Laboratory

Re: [Freesurfer] QDEC and ROI drawing

We don't use qdec in this way, so I don't know. On 04/11/2017 12:38 PM, Arnaud Boré wrote: > Is that normal ? > > Le 11 avr. 2017 12:34 PM, "Douglas N Greve" > a écrit : > > Yes, the label is shifted off the brain when I run

Re: [Freesurfer] QDEC and ROI drawing

Is that normal ? Le 11 avr. 2017 12:34 PM, "Douglas N Greve" a écrit : Yes, the label is shifted off the brain when I run that command On 04/11/2017 10:13 AM, Arnaud Boré wrote: > Hi Douglas, > > Yes I would like to draw ROIs, I understand I can use tksurfer. > I

Re: [Freesurfer] QDEC and ROI drawing

Yes, the label is shifted off the brain when I run that command On 04/11/2017 10:13 AM, Arnaud Boré wrote: > Hi Douglas, > > Yes I would like to draw ROIs, I understand I can use tksurfer. > I would like to know if your fs version has the same behaviour as > mine. I use:

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

Still a bit of a mystery. Can you tar up and send me the rmanova folder? On 04/11/2017 11:18 AM, Clara Kühn wrote: > Oh, yes, sorry: > command line: > mri_glmfit --glmdir > /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/ --y >

Re: [Freesurfer] mris_ca_label giving error CTABfindAnnotation: ct was NULL

when you run mris_ca_train use -t and it will embed it in the .gcs file On Tue, 11 Apr 2017, Das S. wrote: > Hi, > I have created a color table, an annot file and a .gcs file( attached with > the mail). > But when I am trying to execute mris_ca_label with my own .gcs file I am > getting the

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

Oh, yes, sorry: command line: mri_glmfit --glmdir /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/ --y /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh --fsgd

Re: [Freesurfer] QDEC and ROI drawing

Hi Douglas, Yes I would like to draw ROIs, I understand I can use tksurfer. I would like to know if your fs version has the same behaviour as mine. I use: freesurfer-x86_64-unknown-linux-gnu-stable6-20170118 Can you replicate this command line and tell me if the label is well aligned to the

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

sorry, that is the log file. What I want is the terminal output, ie, when you run it, all the stuff that is printed to the screen. On 4/11/17 5:07 AM, Clara Kühn wrote: Hi Doug I am not conciously using a mask but I attached the glmfit.log At the end it actually states "ResidualFWHM -nan"

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

Hi Doug I am not conciously using a mask but I attached the glmfit.log At the end it actually states "ResidualFWHM -nan" How can I fix that? Cheers, Clara - Ursprüngliche Mail - Von: "Douglas N Greve" An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 10.