[Freesurfer] mri_gtmpvc for partial volume

External Email - Use Caution Hello, Can i specify a lookup table when using mri_gtmpvc? This is because I have a non-freesurfer segmentation (MALPEM) and i would like to perform partial volume on it without having to run freesurfer on the subject for PET analysis. I have a lookup

Re: [Freesurfer] Unable to copy the license.txt file into $FREESURFER_HOME

Sent you a reply to your direct email, as attachment I wanted to send is too large for list. - rob On Aug 24, 2018, at 12:40 PM, Tsz Wai (Bentley) Lo mailto:lo...@smh.ca>> wrote: External Email - Use Caution Hi FreeSurfer Developers, I am attempting to copy my license.txt into $FREE

[Freesurfer] Convert mgh to gii

External Email - Use Caution Hi FS experts, I ran surface based analysis between two groups. The final output "is cache.th13.pos.sig.cluster.mgh" I would like to convert this file to gii format using "mris_convert" I tried: mris_convert -c cache.th13.pos.sig.cluster.mgh cache.th

[Freesurfer] Designing Constrats for 3 Group 1 Covariate Analysis

External Email - Use Caution Dear freesurfers, I have what is likely a basic question but I'm new not only to FreeSurfer but contrast matrix design and group analysis as well, and was hoping for some help/clarification. Basically I want to run a GLM on our structural/function

[Freesurfer] Unable to copy the license.txt file into $FREESURFER_HOME

External Email - Use Caution Hi FreeSurfer Developers, I am attempting to copy my license.txt into $FREESURFER_HOME. I have already open a terminal window and define and environment variable called freesurfer_home but I am not sure where FreeSurfer home is. I am not sure how to

Re: [Freesurfer] Error with mris_anatomical_stats

External Email - Use Caution Bruce, this is the output: mri_info wm.mgz Volume information for wm.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.00, 1.00, 1.00 type: UCHAR (0) fov: 256.000 dof: 0

Re: [Freesurfer] Error with mris_anatomical_stats

can you run mri_info on it? And please include the full screen output including the command line that you run as well as what it produces. thanks Bruce On Fri, 24 Aug 2018, Davide Momi wrote: External Email - Use Caution Yes, I meant the second one and rh.aparc.annot (not l

Re: [Freesurfer] Error with mris_anatomical_stats

External Email - Use Caution Yes, I meant the second one and rh.aparc.annot (not lh) given that as you said I specified rh. As for the ls -l on wm.mgz this is the output: -rw---@ 1 davidemomi staff 432151 Jun 13 2017 wm.mgz Thanks Il giorno ven 24 ago 2018 alle ore 17:

Re: [Freesurfer] mri_label2label dependencies

External Email - Use Caution Dear freesurfers, I didn't see a response to this but I might have missed it. In any case it looks like it's working ok. I found an error in what I was doing which was confusing things. Best - Don From: freesurfer-boun...@nmr.mgh.harvard.edu On Beh

Re: [Freesurfer] Error with mris_anatomical_stats

Hi Davide do you mean $SUBJECTS_DIR/mri or $SUBJECTS_DIR/60_AV/mri? It should be the latter, not the former. Also, can you send us the output of ls -l on the wm.mgz? And finally, you probably want to use rh.aparc.annot not lh.aparc.annot since you specified rh on the command line cheers Bruc

Re: [Freesurfer] Error with mris_anatomical_stats

External Email - Use Caution Dear Bruce, thanks for your response. my SUBJECTS_DIR is set to: /Users/davidemomi/Downloads/Broad_60_AV, which is actually where the output of recon-all is located. the file wm.mgz exists and is in the $SUBJECTS_DIR/mri directory Thanks again

Re: [Freesurfer] Error with mris_anatomical_stats

Hi Davide does that file exist? What is your SUBJECTS_DIR set to? cheers Bruce On Fri, 24 Aug 2018, Davide Momi wrote: External Email - Use Caution Dear FreeSurfer, I have a problem when I use mris_anatomical_stats. It gives me an error saying that it couldn't read the i

Re: [Freesurfer] questions about hippocampus subfield error

External Email - Use Caution The subfield part never started. Recon-all died earlier. Andrew: any ideas? -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

Re: [Freesurfer] questions about hippocampus subfield error

External Email - Use Caution Hi Eugenio I did not find the log file you mentioned. Attached is all log file within script directory. Would you please help me to figure out what was wrong? Thank you so much Best wishes Shize 在 2018-08-24 15:50:44，"Iglesias Gonzalez, Eugenio

[Freesurfer] Error with mris_anatomical_stats

External Email - Use Caution Dear FreeSurfer, I have a problem when I use mris_anatomical_stats. It gives me an error saying that it couldn't read the input volume which is the wm.mgz file. would you please help me how I should fix this problem? this is the command which I used:

Re: [Freesurfer] questions about hippocampus subfield error

External Email - Use Caution I am really confused. There are no errors in the subfield module in that log. Can you please send me the file hippocampal-subfields-T1.log, which should be found in the scripts directory (inside the subject’s directory)? Cheers, /Eugenio -- Juan Eugen