Re: [Freesurfer] Hippocampal Subfield Segmentation Error

External Email - Use Caution Hello! So I have installed the latest Java, reinstalled the Runtime following the instructions on the Freesurfer website, and have attempted to remove Java.opts files, to then run the analysis. Still nothing has changed. Any other suggestions? Thank y

Re: [Freesurfer] Tracula: tract length meaning

Hi Nazife - That is correct, the lengths are numbers of voxels along a tract in each subject's native DWI space, so if you were to compare them across subjects you'd probably want to correct for total intracranial volume. (This is just as you would do for any other length/area/volume measurement

Re: [Freesurfer] Error in Tracula-all -prep

Hi Salah - It looks like it didn't find your subject's freesurfer recon when it was doing the pre-processing, so it skipped some steps that you need to go beyond that point. Based on your SUBJECTS_DIR and your subject name, it looked for this file: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/

Re: [Freesurfer] Hippocampal subfields

Dear Ioana, This is tricky because the volumes are computed from soft segmentations, which are not the ones you’re editing. In general, editing outputs is a bad idea; it may be better to simply discard the cases for which quality control fails. Having said that: if you want to use corrected cases

[Freesurfer] Tracula: tract length meaning

External Email - Use Caution Dear Tracula experts, I want to compare two groups according to the length statistics from Tracula overall.stats outputs. I just need comprehensive explanations what "tract length" statistics mean and how they are derived and what their reliability is.

[Freesurfer] Compiling Freesurfer 6 on Centos7 Install not working due to annex files missing

External Email - Use Caution Hi all I’m building Freesurfer version 6 (stable6 branch) in a fresh centos7 OS git clone https://github.com/freesurfer/freesurfer.git cd freesurfer git checkout stable6 git remote add datasrc https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/re

[Freesurfer] Hippocampal subfields

External Email - Use Caution Hello, I'm doing a study about hippocampal atrophy and I'm using the Segmentation of Hippocampal subfields tool. There were some minor errors and I edited them using Freeview, voxel edit tool. I would like to generate a new [lr]h.hippoSfVolumes-T1.v

[Freesurfer] mri_convert input files

External Email - Use Caution Hi, I would like to convert my raw scans to nifty. The scans are made on a Philips scanner. I was able to retrieve most of them as DICOM files, but some of them are only available as PAR/REC. Does mri_convert also handle PAR/REC or can I only conver