Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

mri_cvs_register version for CentOS4 and CentOS5
by tulu＠ms36.hinet.net 06 Jul '11

06 Jul '11

Dear FS experts I download CentOS5 x86-64 version (not CentOS4) of FS 5.1. should I need to upgrade the mri_cvs_register and applyMorph for correction ? best JLH

2 1

Problems with automatic labelling of V1 using the Hinds method in 5.1.0
by Krish Singh 06 Jul '11

06 Jul '11

Hi there, I'm using Freesurfer version 5.1.0 to automatically define labels for left and right V1 using the method outlined in Hinds et al. To do this I add the -label-v1 flag to my recon-all command line. The problem is that this always fails with the following error visible in the .out file: ------------------------------------------------------------------- mris_spherical_average -osurf v1.invivo.reg -n -o 240211-50 label lh.v1.invivo.label lh v1.invivo.reg V1_average /cubric/scratch/CCGG/Freesurf/240211-50/label/lh.v1.prob.label output surface = v1.invivo.reg painting output onto subject 240211-50. processing subject V1_average... MRISreadVertexPosition(white): could not open file /cubric/scratch/CCGG/Freesurf/V1_average/surf/lh.white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory ------------------------------------------------------------------- The problem seems to be with the current version of mris_spherical_average - if I modify the command line above to explicitly execute the old (4.4.0) version of mris_spherical_average then I do not get this error and the script completes without problems. I'd be grateful of any advice/help on this. Best Wishes, Krish -- Prof. Krish Singh CUBRIC School of Psychology / Ysgol Seicoleg Cardiff University / Prifysgol Caerdydd Park Place / Plas y Parc Cardiff / Caerdydd CF10 3AT, UK Tel / Ffôn: 02920 874690 / 870365 Fax / Ffacs: 02920 870339 Email / Ebost : singhkd(a)cardiff.ac.uk

2 3

calculating the surface area of each region on Desikan template
by Zhangyuanchao 06 Jul '11

06 Jul '11

hi, expert, How could I obtain the surface area of each region on the Desikan template? How can I obtain this area in both native space and the average template space? In the surf folder of each subjects, I noticed there is lh.area file, what is meaning of this file? Do I need ?h.area for calculating the area of each region? yuanchao zhang

2 1

tkmedit error message even though tksurfer runs correctly
by Sandy Goncalves 06 Jul '11

06 Jul '11

Hello! I am brand new to this software (and command for that matter) and need some help. After installing all the software, when I enter tkmedit in the xterminal, I receive an error message that looks like this: X Error of failed request: BadRequest (invalid request code or no such operation) ?? ? Major opcode of failed request: 128 (Apple-DRI) ?? ? Minor opcode of failed request: 1 () ?? ? Serial number of failed request: 16 ?? ? Current serial number in output stream: 16 Interestingly, when I type in tksurfer, this works. So I'm not sure what I should do in order to get tkmedit to work! Any help would be great! Thanks, Sandy

1 0

Re: [Freesurfer] mri_cvs_register update
by Peter J. Molfese 06 Jul '11

06 Jul '11

Is this significant enough that we should re-run data processed using the standard recon-all stream in version 5.1? Thanks, Peter On Jun 10, 2011, at 3:28 PM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 2 > Date: Fri, 10 Jun 2011 12:59:34 -0400 (EDT) > From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] mri_cvs_register update > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <Pine.LNX.4.62.1106101257120.4547(a)gate.nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > Hi, > > We found a bug in the mri_cvs_register script after the > release. Please, download the new version of applyMorph and > mri_cvs_register from one of the below links for Linux Centos4, > Linux Centos4 x86 64 and Mac Leopard respectively: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4 > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86… > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/mac-leopard-intel > > --Lilla

2 1

having two freesurfer versions at one computer
by Tetiana Dadakova 06 Jul '11

06 Jul '11

Dear list, I would like to install both 5.0 and 5.1 versions on my computer. But I am not sure how exactly I should proceed after downloading the 5.1 (5.0 is already installed). For example, how should I set FREESURFER_HOME, can it be the same for both versions? Also, can I have my 5.0 in /Applications/freesurfer and 5.1 in /Applications/freesurfer5.1/freesurfer ? Thank you, Tanja.

2 1

MRI registration
by Zeynep Akalin Acar 06 Jul '11

06 Jul '11

Hi all, I'm trying to register two brain volumes using Freesurfer. I need to find a mapping for each voxel of the MR image to the reference image. I tried using mri_register with the option -vf as the wiki documentation suggests that it outputs a vector field. Instead it expects a variance volume. The surface registrations do not work for me either, because they don't include a mapping of inner points. I tried Talairach transformation, but, it is a rigid registration, and I need a non-rigid registration. Is there a tool in Freesurfer that can register two brain volumes with a mapping of each voxel? Thanks, Zeynep.

3 2

stats on masked functional data
by Ritobrato Datta 05 Jul '11

05 Jul '11

Hello All, I have a functional beta value overlay as a .mgh file and a label file and I want to compute the average value within that mask for each subject. Is there a program to do that ? Thanks Ri

4 4

gyrification Index of a label
by Ritobrato Datta 05 Jul '11

05 Jul '11

Hi All, I have run recon-all -s <subj> -localGI Now I want to get the gyrification Index of a particular label. Is there a way to do that ? Please let me know Thanks Ri

3 3

fieldsign problems
by Michelle Umali 05 Jul '11

05 Jul '11

Hi All, I am running a retinotopy analysis, and when I look at the fieldsign image all I see are a bunch of red and blue speckles. Is this normal? Thanks. Michelle

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