Re: [Freesurfer] Cannot allocate memory mri_glmfit to remove covariates

Thanks Douglas, it works now! On Thu, Aug 25, 2016 at 6:45 AM, Douglas N Greve wrote: > It actually looks like it might be a problem with your covariates.mat > file (MatrixReadTxT error). Can you send that file? > > > On 08/22/2016 10:06 PM, Heidi Foo wrote: > > Dear

Re: [Freesurfer] Fwd: Cannot allocate memory mri_glmfit to remove covariates

This looks like it is a binary matlab file. This should be a simple text ascii file. On 8/24/16 9:01 PM, Heidi Foo wrote: Hi Douglas, Attached the covariates.mat file. Thanks. Regards, Heidi Foo -- Forwarded message -- From: *Douglas N Greve*

[Freesurfer] overlapping area question

Hello Freesurfers, I was wondering if someone might have information for how I can measure overlapping areas between a cluster that was generated as a results of a cortical thickness analysis, with a portion of a Yeo Network atlas. Specifically, I would like to calculate the percentage that the

[Freesurfer] Fwd: Cannot allocate memory mri_glmfit to remove covariates

Hi Douglas, Attached the covariates.mat file. Thanks. Regards, Heidi Foo -- Forwarded message -- From: Douglas N Greve Date: Thu, Aug 25, 2016 at 6:45 AM Subject: Re: [Freesurfer] Cannot allocate memory mri_glmfit to remove covariates To:

Re: [Freesurfer] Recon-all error using Freesurfer 6.0

Thankyou! It worked when I removed the trailing " / ". However after it finished running, I received this error: ERROR reading /usr/local/DTI_processed_data/freesurfer_data_dir/fsaverage/label/lh.BA1_exvivo.label Because the "lh.BA1_exvivo.label" file for some reason, when I checked, was

Re: [Freesurfer] GLM surface based cortical thickness analysis vs aparcstat table cortical thickness

Yes, that is possible, but you should see some sort of trend, eg, most the ROI should have a certain sign On 08/24/2016 06:47 PM, miracoo...@gmail.com wrote: > Thanks doug. Also, let's say I extract the aparcstat table and perform t > -test using spss and a ROI become significant, is it

Re: [Freesurfer] GLM surface based cortical thickness analysis vs aparcstat table cortical thickness

Thanks doug. Also, let's say I extract the aparcstat table and perform t -test using spss and a ROI become significant, is it possible the significant effect will be lost using GLM surface based?  Best,  Paul Sent from my BlackBerry 10 smartphone.   Original Message   From: Douglas N Greve

Re: [Freesurfer] Cannot allocate memory mri_glmfit to remove covariates

It actually looks like it might be a problem with your covariates.mat file (MatrixReadTxT error). Can you send that file? On 08/22/2016 10:06 PM, Heidi Foo wrote: > Dear FreeSurfer team, > > I am currently running mri_glmfir --eres-save using FreeSurfer 6.0. > However, there is an error saying

[Freesurfer] freeview error:

Hi FreeSurfer Team, I am trying to edit longitudinal data using FreeView. The original timepoints were processed and edited using FreeSurfer 5.1. The longitudinal data was also ran using FreeSurfer 5.1. I am currently trying to edit the longitudinal data using FreeView, however FreeView

[Freesurfer] I receive an error when running recon-all with T1 and lesions from FLAIR

Dear FreeSurfer team, I'm doing a structural analysis with 50 MS patients and 50 healthy controls (T1, T2 and FLAIR). The MS patients have multiple lesions mainly in white matter. My co-worker did manual editing (bullet points) in the FLAIR images, and i would like to use these edits when

Re: [Freesurfer] FW: Correcting for both hemispheres in thickness analysis using a PFC mask

I've been pushing people to use this method when running monte carlo sims http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo To correct for two hemis, just add --2spaces to the command line. All this does is to bonferroni correct the final clusterwise p-values across two

Re: [Freesurfer] GLM surface based cortical thickness analysis vs aparcstat table cortical thickness

One is a map-based/voxel-wise analysis, each voxel is treated separately. The aparc stats table is an average over all vertices in the ROI. If you have an effect that does goes across the ROI boundary, it could be lost in the ROI analysis. On the other hand, the ROI analysis may be more

Re: [Freesurfer] PET surface sampling

Sample the raw TAC data onto the surface (and not the BPs), then smooth on the surface, then run the mrtm2 with all the same arguments except use the surface data as the input (--y) instead of the ROI data. On 08/23/2016 05:13 PM, Jonathan DuBois wrote: > Hi, > > I’m trying to use the PETsurfer

Re: [Freesurfer] which CUDA version driver to use

On 24 August 2016 at 03:57, Карамфил бахчеванов wrote: > Compiling is something new for me, but will try it. Well, install the binaries, and try that first Richard ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] version 6 NOT released yet

Many thanks! Pedro Rosa. > On Aug 24, 2016, at 13:48, Iglesias, Eugenio wrote: > > You can! It just makes your results harder to reproduce (running recon-all > with one version, and the subfields with the other). > > Juan Eugenio Iglesias > Translational Imaging Group

Re: [Freesurfer] version 6 NOT released yet

You can! It just makes your results harder to reproduce (running recon-all with one version, and the subfields with the other). Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 24 Aug 2016, at 17:01, Douglas

Re: [Freesurfer] version 6 NOT released yet

I don't know. This is a question for Eugenio On 8/24/16 11:53 AM, pedrogomesr...@gmail.com wrote: Hi, Doug. Is it possible to run FreeSurfer 6 Hippocampal-subfields on FreeSurfer 5.3 recons, or this also should not be done? Best, Pedro Rosa. On Aug 24, 2016, at 11:58, Douglas Greve

Re: [Freesurfer] version 6 NOT released yet

Hi, Doug. Is it possible to run FreeSurfer 6 Hippocampal-subfields on FreeSurfer 5.3 recons, or this also should not be done? Best, Pedro Rosa. > On Aug 24, 2016, at 11:58, Douglas Greve wrote: > > > PLEASE DO NOT USE ANYTHING LABELLED AS "6.0" FOR ANYTHING OTHER

Re: [Freesurfer] Fs 6.0 dev version update

Hello Renata, As far as I know, the only change between those two versions was a bug fix that related to the number of arguments based to the longitudinal component of the HippoSF code. If you didnt encounter this error before than I dont think anything would change for you. HOWEVER, I must

Re: [Freesurfer] Fs 6.0 dev version update

Hi Douglas, Thank you for the quick response. Maybe I didn't explain it well enough, I am downloading it from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ I know it is the developmental version, but we are looking at the subregions and that's the only way we can. My question

Re: [Freesurfer] Fs 6.0 dev version update

Hi Renata, version 6 is not ready and should not be used. As far as we know, there is not a link to 6.0 anywhere on our web pages. Where did you find it? doug On 8/24/16 5:48 AM, Vaz pandolfo, Renata wrote: Dear FS experts, I downloaded the FS 6.0 dev version for Linux on 11.08.2016 and

[Freesurfer] ROI-based laminar BOLD analysis

Dear FreeSurfer team, My name is Alex Wilks, an undergrad in the fMRI lab at the University of Michigan. We are trying to learn the ropes of FreeSurfer so that we may be able to perform high resolution fMRI analysis across multiple cortical layers. So far, I have understood how to generate

Re: [Freesurfer] dmri_poistats

Hi Mohamad - This tool hasn't been worked on for over a decade, and there is nobody here who can support it. There are tools out there that do tractography without anatomical priors (in fact that's approximately all the tools out there), but none in freesurfer at the moment. Best, a.y On

[Freesurfer] version 6 NOT released yet

PLEASE DO NOT USE ANYTHING LABELLED AS "6.0" FOR ANYTHING OTHER THAN TESTING. WHEN WE RELEASE 6.0 WE WILL MAKE AN ANNOUNCEMENT. Thanks The FreeSurfer Team ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] dmri_poistats

Hi Anastasia, This tool is available in (FS 5.3 and FS v6.0) as version 1.0 Beta. But in the paper that I have pointed to, the folks used the version 1.4 of this tool. That's why I am a bit confused. Kindly, are there any tools that can help to do tractography for the corticospinal tract when

Re: [Freesurfer] dmri_poistats

Hi Mohamad - This tool is *way* deprecated. It should not have been included in beta releases. Thanks for bringing this to our attention. a.y On Wed, 24 Aug 2016, Alshikho, Mohamad J. wrote: Dear Freesurfer experts, I would like to inquire about the tool “dmri_poistats”

[Freesurfer] FW: Correcting for both hemispheres in thickness analysis using a PFC mask

Hi, I have a question about correcting for 2 hemispheres in a thickness analysis using a PFC mask. Here are the steps I ran: 1) I ran the analysis in qdec without a mask. 2) I found the mri_glmfit.log file from step 1 and cut out the mri_glmfit command that runs the analysis and replaced

[Freesurfer] output description

Dear FS experts, Is there a complete list of all output files followed by their description? The one I can find online seems to be incomplete (and/or out of date): https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles#A-allOutputFiles For example, the volumes brain.mgz and

[Freesurfer] Fs 6.0 dev version update

Dear FS experts, I downloaded the FS 6.0 dev version for Linux on 11.08.2016 and now I see that there is a new version since the 14th of August. I ran about 20 recon-alls with the 11.08 version and now I am wondering if there were any major changes between that and the new one, and if so,