Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

computing euler number error
by Sidwell, Amanda Burns 06 Nov '17

06 Nov '17

Hello, I ran a recon-all that exited with errors. I have attached the recon-all log. It seems to have stopped in the middle of Aseg stats. Can you help me with what commands to use to pick up where the recon left off? Thanks! Amanda

2 1

License issue
by Danny Deng 06 Nov '17

06 Nov '17

Dear FDs, According to the instructions, I have cut the 4 lines between the “CUT HERE”, copy and past the 4 lines into my license.txt file in the home directory to freesurfer folder as follow: ------------------------------------------------------------------------------------------------------- PART C. MISCELLANEOUS This Agreement shall be governed by and construed in accordance with the laws of The Commonwealth of Massachusetts without regard to principles of conflicts of law. This Agreement shall supercede and replace any license terms that you may have agreed to previously with respect to FreeSurfer. dannytang023(a)gmail.com 33367 *CL6BxmQcdv6k FScW2..sWlD9c -------------------------------------------------------------------------------------------------------- However,when I tried to test my installation using the sample-001, it shows the error message as follow: Xues-MacBook-Air:~ DannyDeng$ cp $FREESURFER_HOME/subjects/sample-001.mgz usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... target_directory Xues-MacBook-Air:~ DannyDeng$ mri_Convert sample-001.mgz sample-001.nii.gz mri_convert.bin sample-001.mgz sample-001.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from sample-001.mgz... -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /Applications/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- Xues-MacBook-Air:~ DannyDeng$ Please help. thanks However Best Regards, Danny Deng

1 0

Helping with convert tool
by Rosalia Dacosta Aguayo 05 Nov '17

05 Nov '17

Dear FreeSurfer list, My name is Rosalia and this is the first time I post an email on your list. I have never run FreeSurfer before and I have a doubt regarding the converting process. For every T1 folder, I have 192.ima files. I do not know how to pass from this point to .mgz. It seems that in the tutorial you are speaking about converting one .dcm file to .mgz file. In my case, I have 192 .ima files and I do not know how to pass them to one .dcm file and then to .mgz file. Even, I am not sure if I could work with .nii.gz files instead of .mgz because I know that my .nii.gz files are well oriented but I do not know if my .mgz files will have any orienting problem. I would be more than grateful if you could kindly help me with this question. Kind regards, Rosalia

2 1

Question about Xhemi
by lanbo Wang 05 Nov '17

05 Nov '17

Dear Freesurfer experts, When I try run mris_apply_reg according to Xhemi: "the error is lh.map.mgh does not exist or is not readable by you" lh.map.mgh is made by which step? Thank you in advance. best, Lanbo

2 2

mris_apply_reg
by lanbo Wang 05 Nov '17

05 Nov '17

Dear Freesurfer experts, I try run this code according to Xhemi： mris_apply_reg --src-label label/rh.V1_exvivo.thresh.label --trg rh-on-lh.V1_exvivo.thresh.label \ --streg xhemi/surf/lh.fsaverage_sym.sphere.reg surf/lh.fsaverage_sym.sphere.reg However, error shows: Option --src-label unknown. And also mris_apply_reg --help didn't show how to correctly use -label. What's the correctly code. Thanks for your advices. Best, Lanbo

3 3

Fwd: bug report
by Danny Deng 05 Nov '17

05 Nov '17

> Dear Freesurfer developers, > > I encountered a problem when I tried to open the sample-001. with information as follow: > > ERROR: Invalid FreeSurfer license key found in license file /Applications/freesurfer/license.txt > If you are outside the NMR-Martinos Center, > go to http://surfer.nmr.mgh.harvard.edu/registration.html <http://surfer.nmr.mgh.harvard.edu/registration.html> to > get a valid license file (it's free). > If you are inside the NMR-Martinos Center, > make sure to source the standard environment. > > In fact I have already saved the license and directed from the desktop into my home directory. > > Please help. thanks so much! > > > Best Regards, > Danny Deng Best Regards, Danny Deng > Begin forwarded message: > > From: Danny Deng <dannytang023(a)gmail.com> > Subject: bug report > Date: November 5, 2017 at 9:04:43 PM GMT+8 > To: freesurfer(a)nmr.mgh.harvard.edu > > Dear Freesurfer developers, > > I encountered a problem when I tried to open the sample-001. with information as follow: > > ERROR: Invalid FreeSurfer license key found in license file /Applications/freesurfer/license.txt > If you are outside the NMR-Martinos Center, > go to http://surfer.nmr.mgh.harvard.edu/registration.html <http://surfer.nmr.mgh.harvard.edu/registration.html> to > get a valid license file (it's free). > If you are inside the NMR-Martinos Center, > make sure to source the standard environment. > > In fact I have already saved the license and directed from the desktop into my home directory. > > Please help. thanks so much! > > > Best Regards, > Danny Deng >

2 3

Extracting lGI Values
by Nguyen, Tin 05 Nov '17

05 Nov '17

Hello, I am attempting to extract lGI values (i.e., similarly to *.stats in #SUBJ/stats) with the following (generic) command: $mris_anatomical_stats –a aparc.annot –t pial_lgi –f #SUBJ/stats/lh.aparc_lgi.stats #SUBJ lh However, this newly generated lh.aparc_lgi.stats is the exact same as the lh.aparc.stats, which is originally and readily in the /stats folder, and does not contain values for lGI. Thus, I cannot proceed with aparcstats2table to write and export the values. I have read through this thread [https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-November/016339…] but it did not seem to help since the demonstrated results were to out thickness. Thank you for your assistance! -Tin

1 0

VBM question
by Mohamed Ali Bahri 05 Nov '17

05 Nov '17

Dear Freesurfer users, I would like to study the between groups changes of volume/cortical thickness of one region (Perirhinal) belonging to the Brodmann areas. I tried to do that with Qdec tool but unfortunately Qdec does not load the Brodmann areas stat list. I am wondering if I could use the GLM formalism with of course regressing out the ITV. Any suggestion/advice will be very welcome. Many thanks in advance, Best regards, Mohamed -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Cyclotron Research Centre, University of Liège, Belgium m.bahri(a)uliege.be

4 3

Re: [Freesurfer] Occipital flattening
by Patricia Stefancin 03 Nov '17

03 Nov '17

ls -l *patch* output: -rw-rw-r-- 1 tstefancin analyses 723208 Oct 26 14:38 lh.occip.patch3d -rw-rw-r-- 1 tstefancin analyses 646376 Oct 27 09:32 lh.occip.patch.3d -rw-rw-r-- 1 tstefancin analyses 401704 Oct 26 14:25 lh.patch -rw-rw-r-- 1 tstefancin analyses 917832 Oct 26 14:40 rh.occip.patch3d surf]$ mris_flatten -1 -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat using write iterations = 0 sampling 7 neighbors out to a distance of 20 mm mrisFindNeighbors: lh.occip.patch.3d: face[3].v[0] = 0, but face 3 not in vertex 0 face list No such file or directory

2 1

Re: [Freesurfer] Occipital Flattening
by Patricia Stefancin 03 Nov '17

03 Nov '17

I managed to change the directory, but when I ran the mris_flatten command it still said the file could not be found.

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer