[Freesurfer] Question regarding mri_label2label and mris_anatomicalstats

External Email - Use Caution Dear Freesurfer Experts, I am currently doing a Longitudinal LME comparison between early and late onset Parkinson's Patients. After the Matlab analysis, I view the resulting sig.mgh file in tksurfer and create a label based on regions that pass FD

Re: [Freesurfer] GM and WM intensity thresholds (Manual Edits)

Hi David 1. I think the main function of the 3T flag is to align to an Talairach average of 3T data, so probably you should continue to use it. 2. There really is no hard threshold. For the control points you want to use voxels that are entirely wm , no partial voluming and no pathology. 3.

Re: [Freesurfer] re-run fsaverage only

Hi Ryan the fsaverage we distribute with freesurfer is static, not created from your study (unless you do so explicitly with the make_average_subject script). What is different between the old and new ones? cheers Bruce On Tue, 27 Nov 2018, Ryan Wales wrote: External Email - Use

[Freesurfer] GM and WM intensity thresholds (Manual Edits)

External Email - Use Caution Hello FreeSurfer Experts! I currently supply inhomogeneity-corrected (via N4 biascorrection) 3T T1w scans through recon-all pipeline. The correction has solved many segmentation errors which reduced the time spent on manual editing. I have several ques

Re: [Freesurfer] CerebralWhiteMatterVol {Disarmed}

External Email - Use Caution Hello, I had a follow up question regarding the CerebralWhiteMatter variable from aseg.stats. 1. Does this include the white matter underlying the cortex? 2. How about the subcortical white matter? (For example, I noticed that there w

[Freesurfer] Running selxavg with many (~5000) different conditions

External Email - Use Caution Hi, I'm currently running an analysis that requires defining each of 5000 stimuli as a condition during processing, and for each subject, I have about 140 runs. As a result, selxavg is taking a very long time and huge amounts of memory to run. F

[Freesurfer] re-run fsaverage only

External Email - Use Caution Hello, I accidentally renamed my fsaverage directory when I was renaming my subjects' directories. Since I was still in the process of running subjects, a new fsaverage directory was automatically created. Now I have two fsaverage directories that each

Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz

External Email - Use Caution I tried to put the subject folder in tar.xz format for ease, this is what I get: ftp> put /home/gorkem/output/BE2.tar.xz local: /home/gorkem/output/BE2.tar.xz remote: /home/gorkem/output/BE2.tar.xz 200 PORT command successful. Consider using PASV. 553

Re: [Freesurfer] Two problematic participants -- unable to run recon-all

instructions are here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Tue, 27 Nov 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Caution Hi Bruce, Could you send me a link to upload one subject? I have never done this before. Thank you, Rosalia El

Re: [Freesurfer] Two problematic participants -- unable to run recon-all

External Email - Use Caution Hi Bruce, Could you send me a link to upload one subject? I have never done this before. Thank you, Rosalia El mar., 27 nov. 2018 16:08, Bruce Fischl escribió: > Hi Rosalia > > if you tar and gzip the entire subject folder of one of the problematic

Re: [Freesurfer] Two problematic participants -- unable to run recon-all

Hi Rosalia if you tar and gzip the entire subject folder of one of the problematic subjects and put it on our ftp site we will take a look. Alternatively, you can take a look at this tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview which should help

[Freesurfer] Two problematic participants -- unable to run recon-all

External Email - Use Caution Dear Free Surfer experts, I have run recon-all for all my participants and I am editing the brainmask and making control points. I have seen that for two participants, Free Surfer were not run. I run those two participant again and I saw that they were

Re: [Freesurfer] segmentHA_T2.sh: amygdala recon-all command stoped.

External Email - Use Caution While I guess it’d technically be possible to use the SAMSEG tools to obtain an initial ASEG, and then modify the hippocampal tool slightly to accommodate this change, I think that I’ll say that no, at this moment it is not possible – but maybe we sh

[Freesurfer] mean LGI per hemisphere

External Email - Use Caution Dear Freesurfer developers, I have a quick question regarding calculating mean LGI (Marie Schaer's measure) per hemisphere. I believe that I can get the mean LGI per hemisphere with a command like: mri_segstats --slabel subject_ID lh $SUBJECTS_DIR/s

Re: [Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

External Email - Use Caution Hi Douglas, Thanks a lot for your answers. 1) For the permutations, would you recommend using this for controlling for MC in cortical thickness analyses too? Why is it recommended to use permutation simulation as opposed to Z Monte Carlo simulation

Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz

External Email - Use Caution Hello Bram, I just followed the guideline at FTPFileExchange, put them to transfer/incoming. Files I put are: 001.mgz rawavg.mgz build-stamp.txt recon-all-status.log recon-all.cmd recon-all.env recon-all.error recon-all.local-copy recon-all.log error.