Freesurfer November 2017

freesurfer@nmr.mgh.harvard.edu

110 participants
198 discussions

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

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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 >

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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

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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

RE : Occipital Flattening
by Patricia Stefancin 03 Nov '17

03 Nov '17

When I run the command pwd it shows me as being in the home file, but I have repeatedly changed the directory to the subject's surf folder. Why is it not changing the directory?

1 0

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

03 Nov '17

Hi again, I ran the command you send and the output is as follows ls cannot access *patch* : no such file or directory

2 1

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

03 Nov '17

Hi Bruce, Here is the command line and the output. mris_flatten -1 -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat MRISread(lh.occip.patch.3d): could not open file No such file or directory mris_flatten: could not read surface file lh.occip.patch.3d No such file or directory

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Freesurfer November 2017