[Freesurfer] Analyze to nii convertor

Dear All, I have a set of images with analyze 75 (img/hdr) format. I want to convert them to .nii single file format. I used the following command: mri_convert -i name_of_input_file -it analyze -ot nii -o name_of_output_file But the output file has not proper nii format, When I drag the file

Re: [Freesurfer] New User - Gyrification Index question

I am still trying to find the right command line approach to running recon -all. I am sure this is documented somewhere - any pointers? Do I have to set any environment variables like FREESURFER_HOME etc.for each terminal I try to run freesurfer? Also, can my images be on Google Drive when I try

Re: [Freesurfer] Questions about eTIV

Hi Niklas, I cannot answer your question on the 4dfp suite, but want to point you at http://www.freesurfer.net/fswiki/eTIV It says that newer version in FreeSurfer "use the atlas $FREESURFER_HOME/average/711-2C_as_mni_average_305.4dfp.img and the registration to that atlas is found in

Re: [Freesurfer] How to calculate the volume of subcortical structure using my own atlas?

Hi Tianqi you mean you want to warp your atlas onto a subject, then measure the volume of the warped structures? You can certainly do that, but in general we have found it to be less accurate than explicit segmentation. Note that mri_vol2vol doesn't compute a transform, it just applies one.

[Freesurfer] GLUT: Fatal Error in tksurfer.bin

Hi list, I have installed FS on my macbook (el capitain) and this error occur:tksurferGLUT: Fatal Error in tksurfer.bin: could not open displayI have look in previous mail in the forum but, although the error has been already discussed, no solution for my issue I have

[Freesurfer] Questions about eTIV

Dear FreeSurfer team, I am writing a paper about FreeSurfer's estimates of intracranial volume (eTIV), when using FreeSurfer version 5.3.0, and have two questions that I would be very grateful if you could answer. My understanding is that the alignment (from which the atlas scaling factor is

Re: [Freesurfer] GLUT: Fatal Error in tksurfer.bin

Hi Stefano can you run other x applications (e.g. xclock, xeyes) from the same window? This sounds like an X error, not anything to do with us cheers Bruce On Wed, 20 Jan 2016, std...@virgilio.it wrote: Hi list,  I have installed FS on my macbook (el capitain) and this error occur:

[Freesurfer] Regressing out various categorical variables

Dear Freesurfers, I am running a design in which I want to correct for a number of categorical variables: diagnosis, gender and apoe status and one continuous variable (age) in a correlation analysis Did I get this right? (below) Thanks, Eric GroupDescriptorFile 1 Title MyTitle Class

[Freesurfer] How to calculate the volume of subcortical structure using my own atlas?

Dear freesurfers, I want to calculate the volume of subcortical structure using my own atlas. But my altlas is not in the fsaverage space. In order to achieve my goal, I plan to use the mri_vol2vol command to register my atlas to the fsaverage subject and then register every subject to the

Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

Thank you for the reply Douglas, Factor 1 (diagnosis) has 3 levels (BPD, CCP, NPC). I created using the vi editor, one line for each level. Same as factor 2. Max On dijous 14 gener 2016 22:20 CET, Douglas N Greve wrote: > how many levels does factor 1 have?