Re: [Freesurfer] localGI problems

Thank you Doug, anyway I'm afraid I still have problems with the recon-all -localGI. After answering *yes *to the removal of the temporary file, it seems that the program stops without doing anything. Now my *tmp* folder contains just one file (*edit.dat*). Below you can see what I see from my ter

[Freesurfer] Get mean thickness after qdec monte-carlo simulation.

Dear surfers. I’ve analyzed 2 group comparison data using qdec gui. I got some significant clusters after Monte-carlo simulation with 1.3, absolute. However, I have no idea to get thickness value of each group in the significant areas. Is there any way to extract mean (and S.D. if possible) thick

Re: [Freesurfer] Fwd: surface to volume visualization

Dear Louis, Thank you for your comprehensive response, the QA tools are certainly valuable tools. I'm very curious on how I could go about getting Freeview snapshots without invoking X. I was wondering whether you are happy to share your "alternative version which gets snaps with freeview"? Or per

Re: [Freesurfer] Get mean thickness after qdec monte-carlo simulation.

In QDEC, there is not a way to do this, but you can do it from the command line. If you cd to where the qdec output is (it might be a folder called Untitled in your $SUBJECTS_DIR), then run mri_glmfit-sim --glmdir Untitled --cwpvalthresh .05 --cache 1.3 abs --2spaces This will only take a min

[Freesurfer] Categorical covariates with more than two levels on qdec

Dear Freesurfer experts, I am doing an analysis on a large data set gathered from eight different imaging centres. In my analysis I would like to covary for the imaging site but qdec only allows me to covary for categorical variables if they have two levels (and I have eight). I am also using

Re: [Freesurfer] mris_divide_parcellation for white matter

Hi Bruce, I am trying to do just that using the following command line: mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown --volmask --o ${subj_dir}/mri/wmdivided --annot aparc.split After the slice labeling, I get the following: Used brute-force search on 872 voxels Fixing Parah

Re: [Freesurfer] mris_divide_parcellation for white matter

Hi Corinna you need to give some output extension so it knows what file type to write (e.g. .mgz, .nii, .nii.gz. mgh, ...) cheers Bruce On Wed, 2 Jul 2014, Corinna Bauer wrote: Hi Bruce, I am trying to do just that using the following command line: mri_aparc2aseg --s ${subject} --labelwm -

Re: [Freesurfer] Categorical covariates with more than two levels on qdec

I have similar questions too, Hanna! I tried to select a categorical variable with 3 levels in Discrete (Fixed Factors) tab, but failed. In another analysis, I am trying to select two continuous variables in the Continuous (Covariate) tab, but qdec does not allow me to select two at one time. Do

Re: [Freesurfer] Fwd: surface to volume visualization

Hi James, It's not possible (currently?) to get snapshots with Freeview or the tktools without invoking X. I can post a link for the modified script which uses Freeview instead of the tktools. It's much slower though and until the movie frame capture is a commandline option, using the tktools

Re: [Freesurfer] mris_divide_parcellation for white matter

And then for breaking the individual labels up, would mri_extract_label be the best option? On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl wrote: > Hi Corinna > > you need to give some output extension so it knows what file type to write > (e.g. .mgz, .nii, .nii.gz. mgh, ...) > > cheers > Bruce

Re: [Freesurfer] mris_divide_parcellation for white matter

yes, or mri_binarize --match cheers Bruce On Wed, 2 Jul 2014, Corinna Bauer wrote: And then for breaking the individual labels up, would mri_extract_label be the best option? On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl wrote: Hi Corinna you need to give some output extension

Re: [Freesurfer] localGI problems

Hello Elisa, I've seen this issue that the process gets stuck even if you answer the question. That happened to me and others before, see the following posts: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg07251.html http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu

Re: [Freesurfer] recon-all CUDA error

Hi, Turns out if you rename libcudart.so.6.0 to the 5.0 in your respective lib64, you can pass the cudadetect for Freesurfer. However after it will crash with a segfault error. This leads me to believe that I installed correctly. I think Freesurfer only supports up to CUDA 5.0 so far (although

[Freesurfer] (no subject)

Hi Chris, If you could get support for CUDA 5.5 it would be marvelous. I'm quite inexperienced with the CUDA programming (consider me an enduser), you would have my full support. I also have a computer here to do any testing if needed. I have a PC with CentOS 6.5, Freesurfer 5.3.0, i7 4770k, 1

Re: [Freesurfer] mris_divide_parcellation for white matter

Whereby the label name is derived from which, the GM labels? i.e. lh.rostralmiddlefrontal_div3 On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl wrote: > yes, or mri_binarize --match > > > cheers > Bruce > > > On Wed, 2 Jul 2014, Corinna Bauer wrote: > > And then for breaking the individual labels

Re: [Freesurfer] recon-all CUDA error

Hi there, I'm currently working on compiling FS source code trying to use CUDA 6, and newer GPUs like Titan series. I haven't got lucky yet, but I will keep on trying... In the meantime I would like to download the CUDA 5 binaries. Are these binaries been published? I can't find anything on the Fr

Re: [Freesurfer] mris_divide_parcellation for white matter

I figured it out. Thanks for your help! On Wed, Jul 2, 2014 at 2:00 PM, Corinna Bauer wrote: > Whereby the label name is derived from which, the GM labels? i.e. > lh.rostralmiddlefrontal_div3 > > > On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl > wrote: > >> yes, or mri_binarize --match >> >> >

Re: [Freesurfer] recon-all CUDA error

Hi, Thank you for your reply. The CUDA 5.x binaries can be found in the CUDA 5.x legacy drivers for CUDA. As long as you set the PATH=/usr/local/cuda/bin:$PATH and LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH, Freesurfer's cudadetect will look into here for the binaries. I think you

[Freesurfer] Processing then xhemi registration to group healthy hemispheres

Hi, In our analysis of stroke patients, I've followed the recommendation to process images, then flip the final surfaces with xhemi for only the subjects with RH lesions to group all healthy hemispheres together for stati

Re: [Freesurfer] Processing then xhemi registration to group healthy hemispheres

Good to hear you are ready for publication! On 07/02/2014 03:26 PM, Peggy Skelly wrote: > Hi, > > In our analysis of stroke patients, I've followed the recommendation > > to process images, then flip the final surfaces

Re: [Freesurfer] mris_divide_parcellation for white matter

yes On Wed, 2 Jul 2014, Corinna Bauer wrote: Whereby the label name is derived from which, the GM labels? i.e. lh.rostralmiddlefrontal_div3 On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl wrote: yes, or mri_binarize --match cheers Bruce On Wed, 2 Jul 2014, Corinna Bau

[Freesurfer] Longitudinal pipeline + LME question

Hello experts, We are setting out to look at a sample of 10 (subset of eventual larger sample) who have at least 2 sets of MRI. Some have many more than 2. However, some of the scans were done on different scanners (a few on 1.5T versus most on 3T) and with slightly different parameters (namely, d

Re: [Freesurfer] problems with Surface-based Interhemispheric Registration

Hi Doug did you see my mail below? any ideas of where the problem could be? thank you! I am using the 5.0, but I have followed the instructions and downloaded the new files as indicated. the xhemi folder has some folders that are empty (bem, label, src, stats, tmp), while the others include files

[Freesurfer] -normalization all black

Hi Everyone, I would like to normalize some images. But even when I test the -normalize option with recon-all -s burt/ -normalization which from what I can see changes /burt/mri/nu.mgz (which came with the freesurfer download) to /burt/mri/T1.mgz, T1.mgz is entirely black. Is there a way to fi

Re: [Freesurfer] Longitudinal pipeline + LME question

Hi Brianna, Yes, that is the best option in my opinion. You should include field strength as a covariate, and maybe other acquisition parameters. Best Martin Sent via my smartphone, please excuse brevity. Original message From: Brianna Damadian Date:07/02/2014 10:04 PM (

Re: [Freesurfer] Longitudinal pipeline + LME question

Hi Martin, Thanks for the response. What we are trying to do is look at changes within the same subject after a certain date (date of a surgical procedure). Would it make more sense to run all scans before and after this date in the same longitudinal pipeline and then look for differences or to

Re: [Freesurfer] Tracula ERROR: fMRIframe: frame >= nframes

Hi Anastasia, You are right! There are empty spaces at the end of the lines in original bvecs and bvals. I could fix the error and finish trac-preproc without error by eliminating these spaces. Thank you so much! Regards, Jun Shinozaki 2014-07-02 15:21 GMT+09:00 Anastasia Yendiki : > > There are

Re: [Freesurfer] Tracula ERROR: fMRIframe: frame >= nframes

Anastasia, I was finding the same error as Jun, and your help fixed it. Thank you very much. However, I am now finding a new error (attached). Can you help me? Thank you again. Regards, Pedro Rosa. On Wednesday, July 2, 2014 at 10:49 PM, Jun Shinozaki wrote: > Hi Anastasia, > > You are right!

Re: [Freesurfer] Tracula ERROR: fMRIframe: frame >= nframes

Hi Pedro - Have you specified not to do eddy current compensation? It looks like it's being skipped. In that case, you need to also skip the QA step (by adding -noqa to your trac-all command line). That's because the QA step requires the output of the eddy current compensation to assess how mu

Re: [Freesurfer] Longitudinal pipeline + LME question

Hi Brianna, I recommend to run all scans of a patient with one single subject template (base).  Then , if you are interested if atrophy rates change after intervention, you could use a piecewise linear model, with a node at the surgery. You can then compare your change in slopes with the chang