[Freesurfer] monte-carlo error in longitudinal pipeline

Hello Experts, I am running a paired t-test cortical thickness analysis based on the instruction on the wiki page ( https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis). However, the monte carlo files weren't not created when i corrected for multiple comparisons. Below are my script, fsgd

Re: [Freesurfer] recon-all exited with error

Hi Trisanna, Try running 'quote PASV' in ftp before running 'put' - that should hopefully clear up this issue. best, Andrew On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much > wrote: Sorry, Bruce. ignore my

Re: [Freesurfer] recon-all exited with error

Sorry, Bruce. ignore my last email. Not sure what happened there. I now am trying to upload icbm-205.tar.gz (the subject that failed) but I get the following and it happens over and over. Any idea what the problem could be? trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/

Re: [Freesurfer] recon-all exited with error

Hi Trisanna there are a bunch of files, but they all look like they are empty: r--r--r-- 1 ftpftp 0 Jan 17 14:24 ICBM_305.tar -r--r--r-- 1 ftpftp 0 Jan 17 14:41 ICBM_305.tar.gz -r--r--r-- 1 ftpftp 0 Jan 17 15:12 icbm-205.tar.gz cheers Bruce On Wed, 17 Jan 2018,

Re: [Freesurfer] Issues with hippo subfields / amygdala fixed

Got it. Thank you so much for all the information. Best, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School ___ Freesurfer mailing list

Re: [Freesurfer] Hippocampal Sub-field volume units

Short answer: yes, it’s cubic mm. -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of "Crawford, Anna"

[Freesurfer] Hippocampal Sub-field volume units

Hello, i am using the hippocampal subfield segmentation. I am looking at the results in [lr]h.hippoSfVolumes-T1.v10.txt. I saw the following in the FAQs and was unsure of what the units were then in the .txt file. Does the .txt file give units in mm^3? * The sum of the number of

Re: [Freesurfer] recon-all exited with error

Thanks Bruce. I have uploaded it but I would like to confirm that you received the ICBM_305.tar. For some reason I was not able to compress it any further. To clarify, subjects 205 and now subject 202 have both failed after surface extraction. best Trisanna -- Ph.D. Candidate McGill University

[Freesurfer] Cloning Voxel Tool Question

Hi All, I was wondering if someone might be able to confirm about whether cloning a voxel is working right based on my description. My concern stems from the fact that when I follow instructions to clone a voxel from a T1 onto the brainmask, I click on the brainmask but do not see any

Re: [Freesurfer] Issues with hippo subfields / amygdala fixed

Good point, Arkadiy. Essentially, the binaries were expecting the Matlab 2014b runtime to be present, but the rest of scripts were still assuming Matlab 2012b (those are the files that were not committed). This should only have happened if you downloaded the dev version between December 23rd

[Freesurfer] Issues with hippo subfields / amygdala fixed

Dear Dr. Iglesias, Could you please let me know what the specific problems were that are fixed? I am asking because I have already applied this segmentation, and want to make sure that the data is valid. Thank you so much, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow

[Freesurfer] Issues with hippo subfields / amygdala fixed

Dear all, The problems with the hippocampal subfield / nuclei of amygdala module (as well as with the brainstem module) in the dev version should now be fixed. I apologize for the inconvenience these issues might have caused. I rushed to leave everything ready right before the winter break and

Re: [Freesurfer] Cortical White matter/corpus callisum

Hi Elisabetta - Yes it is included in the calculation of the cerebral WM. Since the CC is a WM tract comprising the Forceps Minor and Major, it is part of the WM calculation. best, Alan On Tue, Jan 16, 2018 at 11:58 AM, Del Re, Elisabetta < elisabetta_de...@hms.harvard.edu> wrote: > Alan, >

Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

Hi Martin, I didn't try to run recon-all, I try to run flipped. The code I used is: foreach subject (subj_27_2.long.s27_base) foreach? surfreg --s $subject --t fsaverage_sym --lh foreach? surfreg --s $subject --t fsaverage_sym --lh --xhemi foreach? end Thanks, Lanbo On Tue, Jan 16, 2018 at