Re: [Freesurfer] FreeSurfer v5.1 {Disarmed}

External Email - Use Caution Thanks, that did the trick! From: Tyler Ward Sent: Wednesday, August 12, 2020 8:46 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Hua, Jessica Subject: Re: [Freesurfer] FreeSurfer v5.1 {Disarmed} Hi Jessica, Freesurfer

Re: [Freesurfer] FreeSurfer v5.1 {Disarmed}

External Email - Use Caution Hi Jessica, Freesurfer is actually looking for the file "/Applications/freesurfer/.license", excluding the file extension. You can simply remove the ".txt" extension from the file name such as with: /$ mv /Applications/freesurfer/.license.txt

[Freesurfer] mri_volsynth help

External Email - Use Caution Hi Freesurfers, I'm trying to create a ROI based on peak significance voxel from a paper. They reported a peak at X=21, Y=-71, Z=22 and area of 4,620 mm², based on MNI305. My idea was creating a sphere ROI around this voxel and check its area in the bra

Re: [Freesurfer] FreeSurfer v5.1 {Disarmed}

External Email - Use Caution Hi FreeSurfer, I did the below steps, and I am still getting the same error message. ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to

Re: [Freesurfer] FreeSurfer v5.1

External Email - Use Caution Hello Jessica, I believe the environment variable FREESURFER_HOME should point to where the license.txt file lives.  That is set when you source the freesurfer setup script, e.g., SetUpFreeSurfer.sh, in the terminal window. You can see the wiki

[Freesurfer] mri_glmfit and R

External Email - Use Caution Hello Freesurfer Experts, I am trying to plot the ${meas} values at the maximum vertex in a significant cluster found by the group analysis pipeline (mri_glmfit). I created an .mgh file with mris_preproc, rh.cbd7.area.10.mgh. I read this file into ma

Re: [Freesurfer] FreeSurfer v5.1

External Email - Use Caution Hi FreeSurfer, I was able to find the older versions of FreeSurfer and download v5.1. I am trying to run recon-all and am running into this issue: ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NM

Re: [Freesurfer] hippocampal subfields error

External Email - Use Caution The whole log message: # #@# Hippocampal Subfields processing (T1 only) left Mon Aug 10 18:54:21 EDT 2020 -- Setting up environment variables --- LD_LIBRARY_PATH is .:/

[Freesurfer] FreeSurfer v5.1

External Email - Use Caution Hi FreeSurfer, To be consistent with old analyses, I need to process my data using FreeSurfer v5.1 on my Mac. Do you know where I can find the link to install v5.1? Best, Jessica Hua ___ Freesurfer mailin

Re: [Freesurfer] Local GI error with Matlab

External Email - Use Caution It worked! Thank you so much On Tue, Aug 11, 2020 at 7:33 AM Douglas N. Greve wrote: > Try downloading > https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m > and copying it to $FREESURFER/matlab > > > On 8/10/2020 8:47 PM, Lab of

Re: [Freesurfer] hippocampal subfields error

Dear Courtney, You can safely ignore “This file does not contain MRI parameters”. If the output files are not created, there must be another error further down. Could you please send us the whole output? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSA

[Freesurfer] hippocampal subfields error

External Email - Use Caution We are getting an error after running the hippocampal subfields pipeline that we have never received before. It is happening for all subjects. We run recon-all and then the hippocampal pipeline and the output files are not being created. Below is the be

Re: [Freesurfer] Hippocampal subfields --> normalization

Dear Hae Won, Normalizing by ICV and whole hippocampal volume simply attempt to answer two different questions: Is the volume of subfield X, accounting for head size, [insert analysis question here]? Is the % of hippocampal volume covered by subfield X, [insert analysis question here]? (where [a

[Freesurfer] Hippocampal subfields --> normalization

External Email - Use Caution Hi. team! Recently, I submitted a paper dealing with volumes of hippocampus and its subfields in epilepsy patients who have significantly reduced hippocampal volume (compared with normal controls) and, in that paper, I used the normalization method u