Re: [Freesurfer] [EXTERNAL] Re: Checking number of parcels after transformation of an annotation file into a .nii.gz file

2019-05-24 Thread Winkelbeiner, Stephanie A
External Email - Use Caution Hi Doug, thanks again for the great tip with MRIread - worked perfectly (after gunzipping the parc300.nii.gz). So, this means I have the next problem now: instead of 300 parcels this image contains 638 parcels... How I created parc300.nii.gz: 1.

Re: [Freesurfer] TrackVis question

2019-05-24 Thread Alan Francis
External Email - Use Caution Hi Ruopeng - Thanks for your reply. As you advised, I used the gradients from the collected data and it gave me an error message which is follows: - Launching dti_recon - Volume dimension: 173 207 173 Voxel size: 1.050 1.05

Re: [Freesurfer] Error with mri_glmfit command

2019-05-24 Thread Martin Juneja
External Email - Use Caution Hi Dough, Please find the Xg.dat file attached here. Thanks. On Fri, May 24, 2019 at 7:30 AM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Can you send the Xg.dat file? > > On 5/23/2019 8:43 PM, Martin Juneja wrote: > > External

Re: [Freesurfer] question on surface analysis

2019-05-24 Thread Barletta, Valeria
It worked perfectly, thank you!! From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: Wednesday, May 22, 2019 1:22:30 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] question on surface analysis mri_binarize a

Re: [Freesurfer] XL defect in recon-all

2019-05-24 Thread Greve, Douglas N.,Ph.D.
no, sorry On 5/24/2019 10:19 AM, Barletta, Valeria wrote: That would be great. However, I am launching recon-all -all by entering the environment for freesurfer 6 in my terminal (we still have version 5_3 installed in our computers). So there is no way I can copy the files from the 2nd link in

Re: [Freesurfer] Error with mri_glmfit command

2019-05-24 Thread Greve, Douglas N.,Ph.D.
Can you send the Xg.dat file? On 5/23/2019 8:43 PM, Martin Juneja wrote: External Email - Use Caution Hi FS experts, I want to find clusters showing an association between cortical measures and behavior x6 (sex, age and variables x1-x5 as covariates). My FSGD file looks like: GroupDes

Re: [Freesurfer] XL defect in recon-all

2019-05-24 Thread Barletta, Valeria
That would be great. However, I am launching recon-all -all by entering the environment for freesurfer 6 in my terminal (we still have version 5_3 installed in our computers). So there is no way I can copy the files from the 2nd link in the folder $FREESURFER_HOME/bin (I have no access to that f