[Freesurfer] EasyReg usage

for putting together such amazing tools, Fidel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed

Re: [Freesurfer] mris_register problem: "No such file or directory"

ers. 2015-08-02 18:57 GMT+01:00 Bruce Fischl : > try opening it in tksurfer and see if it complains > > On Sun, 2 Aug 2015, Fidel Alfaro Almagro wrote: > > Hi, >> >> Thanks for the quick answer. >> >> There was no error message in the previous steps. >

[Freesurfer] mris_make_surfaces .out output

Hi all, Is there an explicit way to change the directory of the output file that mris_make_surfaces creates? This command creates a .out file in the directory from which the command was run and the -output flags just allows the user to modify a part in the middle of the name of that file. Cheers

Re: [Freesurfer] mris_register problem: "No such file or directory"

to automatically know if there was a problem in the sphere creation? Cheers. 2015-08-02 16:27 GMT+01:00 Bruce Fischl : > hmm, something seems to be wrong maybe the the ?h.sphere. Can you try > recreating it > cheers > Bruce > > On Sun, 2 Aug 2015, Fidel Alfaro Almagro wrote: &

[Freesurfer] mris_register problem: "No such file or directory"

Hi all, I received an error in one of the steps of recon-all. The error is "No such file or directory" at the end of one of the registration processes. The step was mris_register -curv. The command was: mris_register -curv ../surf/lh.sphere /average/lh.average.curvature.filled.buckner40.tif ../s

[Freesurfer] ?reference(s) supporting DLPFC label

Dear FS community, I'm looking into DLPFC volume/thickness. Following advice posted before on this forum, I'm adding G_frontal_middle.label + S_frontal_inferior.label + S_frontal_middle.label from Destrieux 2009 atlas as a surrogate for DLPFC. My question is whether folks could provide referen

[Freesurfer] kvl binaries missing from ppc 5.1 stable release

t. Thanks, Fidel On 20-Aug-12, at 8:48 AM, Nick Schmansky wrote: Fidel, I don't know why those files are missing from the Tiger ppc distribution, but i confirmed that indeed they are. Here is a tarball of the distribution which contains everything: ftp://surfer.nmr.mgh.harva

Re: [Freesurfer] tcsh: tailarach_avi: Command not found

Thanks a lot Nick. It worked like a charm: "recon-all -s struct_FS finished without error at Thu Aug 23 03:52:39 PDT 2012 done" For other users whose OS automatically unzips the .gz, the command to type is: sudo tar xvf freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar Than

Re: [Freesurfer] tcsh: tailarach_avi: Command not found

Hi, I'm reposting this, hoping Nick has returned and can provide some guidance. Thanks, Fidel On 1-Aug-12, at 8:16 AM, Douglas N Greve wrote: > This is strange, it must be something that is specific to the PPC > Mac distribution. Nick is going to have to deal with this, but h

Re: [Freesurfer] tcsh: tailarach_avi: Command not found

mand not found) when I run recon-all. > Do you have permission to install it in that location? I do. Could this be related to compillation of files for the May 2011 5.1. stable release for ppc? Appreciate your advice and support as I understand ppc machines might not be one of the highest p

Re: [Freesurfer] tcsh: tailarach_avi: Command not found

Hi Doug,I re-installed freesurfer, and I still get the same error message (terminal output attached); bin files are still missing from bin folder.Shall I report this as a bug?Regards,Fidel Last login: Tue Jul 31 12:51:32 on ttyp2 Welcome to Darwin! a3128u:~ FVila$ export FREESURFER_HOME

Re: [Freesurfer] tcsh: tailarach_avi: Command not found

Hi Doug. The missing files are NOT in $FREESURFER_HOME/bin; So, I guess that's why they are not found even though the path is set up in the system PATH variable. Suggestions? Fidel Are the missing files in $FREESURFER_HOME/bin and is that path in your system PATH variable? On 07/26/20

Re: [Freesurfer] tcsh: tailarach_avi: Command not found

ciate it.Many thanks, Fidel{\rtf1\ansi\ansicpg1252\cocoartf949\cocoasubrtf540 {\fonttbl\f0\fswiss\fcharset0 Helvetica;} {\colortbl;\red255\green255\blue255;} \margl1440\margr1440\vieww25400\viewh16080\viewkind0 \pard\tx566\tx1133\tx1700\tx2267\tx2834\tx3401\tx3968\tx4535\tx5102\tx5669\tx6236\tx6803\ql\qna

[Freesurfer] tcsh: tailarach_avi: Command not found

Hi Freesurfer experts, I recently installed FS (PowerPC architecture version available on FS website) on a Mac OS X 10.4.11 and I get the attached output error when running recon-all. Advice on how to troubleshoot this would be appreciate. Thanks, Fidel a3128u:/Applications FVila

[Freesurfer] qdec.table.dat file

ormatting. What would be your suggestions to troubleshoot this? Thanks! Fidel qdec.table.dat Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The inform

[Freesurfer] Number of entries error in trac-all

and bvecs files attached. As far as I can see, they have the same number of rows, so... What is the problem? Thanks and best regards, Fidel. 0 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 0.000 0.5095810 0.5610829 -0.6546342 0.1369828 -0.2633449 -0.6291046 -0.6616548 0.69198

[Freesurfer] bash freesurferstats2table script

Hi there, I was wondering if it would be possible to obtain a copy of the freesurferstats2table script that is posted on the Wiki. When I try to access it it requests a user name and password (I tried my mailing list username and psswd, but didn't work). Greatly appreciate it,

Re: [Freesurfer] Smaller Virtual Machine

So... What about this? Cheers :) El 29/04/2011 16:43, Pedro Paulo de Magalhães Oliveira Junior escribió: I'll check if it's public On Fri, Apr 29, 2011 at 11:40, Fidel <mailto:falf...@hggm.es>> wrote: Thanks PPJ, I have made a fast search in Amazon's p

Re: [Freesurfer] Smaller Virtual Machine

Thanks PPJ, I have made a fast search in Amazon's page and via google and I did not find it. Do i have to be registered to find it? Can anyone use a copy of your virtual machine, or do we have to create our own and then, upload it to Amazon? Thanks again. Fidel. El 29/04/2011 16:25,

[Freesurfer] Smaller Virtual Machine

communication. Is anybody thinking about creating a lighter version of this virtual disk image? Thanks and best regards, Fidel. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] Equivalent labels

Thanks to both of you. Cheers. > no we haven't done them > On Wed, 12 Jan 2011, Christophe Destrieux wrote: > >> I meant : am i right to think that we don't have any other parcellation >> available showing the other labels Fidel would like to use ? >> (I

Re: [Freesurfer] Equivalent labels

Hi mr Destrieux, Does this mean that those structures cannot be found in ANY segmentation or labelling made by freesurfer? Thanks again for your quick answer, Fidel. > Hi Fidel > > as stated in the paper you cited, the intralimbic gyrus is made of : > prehippocampal rudiment, indu

[Freesurfer] Equivalent labels

t; but the information there is not useful (e.g. indusium griseum does not appear in that file). Thanks and best regards. Fidel. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesu

Re: [Freesurfer] (no subject)

does not seem to work. Does anybody know how can I do this? Thanks in advance. Fidel. > Thank you very much for the quick answer and happy holidays. > >> Forwarding a previous answer from doug. I tried it before (and >> recently). It does seem to work. >>

Re: [Freesurfer] (no subject)

ital/parietal lobes based off the ? >>>>> h.aparc.annot >>>>> files in a FS 'label' dir? Ideally speaking, I'd like to have a >>>>> ?h.lobar.annot with corresponding lobar.annot.ctab. >>>>> >>>>> Apologies if this question

Re: [Freesurfer] (no subject)

there any tool in the freesurfer suite to allow me to get a segmentation of the different lobes of the brain? Thanks. > Hi Fidel, > > that is deprecated code. What are you trying to do? > > cheers (and happy holidays) > > Bruce > On Fri, 24 Dec 2010, > FIDEL ALFARO ALMAGRO

[Freesurfer] mri_mark_temporal_lobe

Happy holidays for those who celebrate it today, Hi. Is there any documentation on how to use mri_mark_temporal_lobe application and what is its output? I cannot find any. Thanks in advance. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] (no subject)

Happy holidays for those who celebrate it today, Hi. Is there any documentation on how to use mri_mark_temporal_lobe application and what is its output? I cannot find any. Thanks in advance. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu ht

Re: [Freesurfer] Sulci segmentation

Hi Fidel > > the surfaces of the same hemi for a given subject area all topologically > equivalent and share an index structure. what that means is that the > vertex label/annotation can be shown/used on any surface, including the > ?h.white and ?h.pial surfaces (which is probably

Re: [Freesurfer] Sulci segmentation

lated -aparc > > will bring up and show the lh.aparc.annot on top of the inflated > surface. You can also load them from the tksurfer interface using > file->label->import annotation > > cheers > Bruce > > On Mon, 20 Dec 2010, FIDEL ALFARO ALMAGRO wrote: > >> &

[Freesurfer] Sulci segmentation

Hi, I am pretty new in freesurfer and I do not know if this question has been answered before (It is difficult to search for 1 basic question), so I will post it anyways: - Is there any segmentation/labeling in freesurfer that allows the user to identify all the sulci of an MR image? I have done