Re: [Freesurfer] DTI Batch Processing with Tracula

Hi Emily - Can you please send your configuration file and trac-all.log? It's impossible to tell what's going on without seeing those. For now the b-values and gradient vectors are assumed to be the same for all subjects, so you enter only one of each. The code is not set up to run in parallel

[Freesurfer] DTI Batch Processing with Tracula

Hello, I had some questions about setting the dmrirc file for batch processing for DTI. I set the subject list I put in the 6 subjects I wanted to process. Then in the dcmlist I put in the pathway to the data files for each subject. I put a space in between each subjects pathways. Then I put

Re: [Freesurfer] -autorecon 3 error: error reading surf/lh.sphere

just remove it and rerun recon-all with -make all. Something went wrong during write, maybe a full partition, maybe a network glitch, we'll never know cheers Bruce On Fri, 8 Nov 2013, Adam Mezher wrote: Absolutely, sorry about that, the group is now cc'd. the ls -l says: -rw-rw-r-- 1 vhasfcw

Re: [Freesurfer] -autorecon 3 error: error reading surf/lh.sphere

Absolutely, sorry about that, the group is now cc'd. the ls -l says: -rw-rw-r-- 1 vhasfcwui cind 0 Nov 6 15:57 lh.sphere so it has 0 size to it, and I can't open it in tksurfer -bash-3.2$ tksurfer PPMI_290_S_3829m12_i395612 lh sphere Using Freesurfer version 5.1. subject is PPMI_290_S_38

Re: [Freesurfer] glm_fit --prune

Yes thanks so much, it worked very fine Celine > > In that case, I think you will want to change the design at each voxel > based on which subjects are present. I have not tried to do this with > pvr, but there is no reason it should not work. To do this, create a > binary volume from your data th

Re: [Freesurfer] -autorecon 3 error: error reading surf/lh.sphere

Hi Adam can you check to make sure that the partition isn't full? Bruce On Fri, 8 Nov 2013, Adam Mezher wrote: Hi FreeSurfer experts, I am repeatedly running into an autorecon3 error (see below). Any ideas how to fix this? It appears that the software is having an issue reading /surf/lh.sp

[Freesurfer] -autorecon 3 error: error reading surf/lh.sphere

Hi FreeSurfer experts, I am repeatedly running into an autorecon3 error (see below). Any ideas how to fix this? It appears that the software is having an issue reading /surf/lh.sphere and immediately exits afterward. Thank you, Adam *Adam Mezher* Staff Research Associate II Center for Imagin

Re: [Freesurfer] glm_fit --prune

In that case, I think you will want to change the design at each voxel based on which subjects are present. I have not tried to do this with pvr, but there is no reason it should not work. To do this, create a binary volume from your data that has the 0s in it, something like mri_binarize --i

Re: [Freesurfer] sulci depth in table

use -m mean doug On 11/08/2013 02:26 PM, Tara Ann Miskovich wrote: > I see thank you, and what would I use as the measure? Because for > asegstats2table I chose between volume and mean correct? Sorry a bit new at > this. > > Tara > > - Original Message - > From: "Douglas N Greve" > To:

Re: [Freesurfer] sulci depth in table

I see thank you, and what would I use as the measure? Because for asegstats2table I chose between volume and mean correct? Sorry a bit new at this. Tara - Original Message - From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, November 8, 2013 1:00:18 PM Subject: Re

Re: [Freesurfer] sulci depth in table

If you are using mri_segstats then you should use asegstats2table doug On 11/08/2013 11:35 AM, Tara Ann Miskovich wrote: > Hello, > > I am extracting sulci depth using the following > > mri_segstats --annot ${subject} lh aparc --sum lh.sulc.sum --i surf/lh.sulc > > Do you know how I could put th

[Freesurfer] recon all error

Greetings Freesurfers! recon-all -s XXX_SurferOutput exited with ERRORS These are the errors in the log: Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 I would really appreciate any advice! Thank you very much,

Re: [Freesurfer] glm_fit --prune

you will want to use the -no-prune flag.If thisis a group analysis, you should be very, very careful that you know what you are doing. In general, setting values to 0 prior to group analysis will create biased results. What you really need to do is have adifferent model for each voxel that inc

[Freesurfer] glm_fit --prune

Hi, When using glm_fit with an input volume that has many voxels with a 0 value (due to a previous thresholding for quality reasons), and the voxel removes might be distributed randomly across our population, is there a way not to take into account those voxels in the glm_fit model? I saw the --pun

[Freesurfer] sulci depth in table

Hello, I am extracting sulci depth using the following mri_segstats --annot ${subject} lh aparc --sum lh.sulc.sum --i surf/lh.sulc Do you know how I could put this into aparcstats2table? Thank you, Tara ___ Freesurfer mailing list Freesurfer@nmr.mg

Re: [Freesurfer] saving in GIFTI .func.gii format

Hi Shahin, You can use mri_convert to convert the mri_glmfit output to GIFTI (.gii). -Louis On Fri, 8 Nov 2013, SHAHIN NASR wrote: Hi Surfers     I have done a surface-based group-averaged mapping and now I need to save the results of the mri_glmfit (sig.nii) command in GIFTI .func.gii format. 

[Freesurfer] Automated batch ROI

Dear Freesurfer experts, I am about to start an analysis where we will be drawing surface ROIs using the select_talairach_point option, making a label of the vertex selected, and dilating it a set number of times. Each subject has 19 ROIs and we have around 50 subjects. I was wondering if anyone k

[Freesurfer] saving in GIFTI .func.gii format

Hi Surfers I have done a surface-based group-averaged mapping and now I need to save the results of the mri_glmfit (sig.nii) command in GIFTI .func.gii format. Does mri_glmfit support this output format? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Har