Freesurfer November 2009

freesurfer@nmr.mgh.harvard.edu

92 participants
135 discussions

Running mris_volmask to create different resolution ribbon.mgz
by Matt Clarkson 10 Nov '09

10 Nov '09

Dear FreeSurfer I would like to generate ribbon.mgz at different resolutions. The mris_volmask help message says the ribbon.mgz should be the same resolution as brain.mgz, so I replaced brain.mgz with higher and lower resolution versions, and ran mris_volmask <subject> expecting to see different resolution ribbon masks on the output, but the output is always 256x256x256. Is there a way I can do this? Many thanks in advance. Matt Clarkson Senior Research Associate Dementia Research Centre UCL Institute Of Neurology Queen Square London WC1N 3BG m.clarkson(a)ucl.ac.uk Tel: 08451 555 000 ext. 723653 Fax: 020 7676 2066

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a question about the retinotopy mapping
by Huiguang He 10 Nov '09

10 Nov '09

Hi, Dear Experts: *I am trying to use FsFast to do retinotopy analysis and have been following the **instructions at: ** https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis * * It sees that I can get some visulization results through these scripts* * However if I need further analysis, for example, I want to extract V1, V2 and calculate their area value, and then compare the normal control with the amblyopia. * * which kind of scripts should I use?* ** * I also want to know the output directory structure:* * There are ~/rtopy/eccen fieldsign polar directory, is there any document describe what's the meaning of the output directly and files.* * Thanks very much!* * Huiguang* ** * Huiguang He, Ph.D.* *Institute of Automation, Chinese Academy of Sciences.* * *

1 0

Circle around vertex
by Yigal Agam 09 Nov '09

09 Nov '09

Hi, In surface-based analysis, is it possible to create an ROI label that is a circle of a certain radius around a given vertex? Thanks, Yigal

4 7

updating to aparc.a2009s
by SHRIKANTH KULASHEKHAR 09 Nov '09

09 Nov '09

Hi !! I am currently using FreeSurfer version Stable 4. I want to update my annotation files from aparc.a2005s to the latest aparc.a2009s atlas. How can I re-create just the annotation files from the existing files, without having to redo the entire recon-all process ? Re-creating using Stable v4.5. Thank you. Shriks The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/

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Books on Freesurfer
by Rajagopalan, Venkateswaran 09 Nov '09

09 Nov '09

Hello, I am new to the field of cortical thickness analysis and freesurfer software. I looked at the tutorials (mainly Powerpoint slides and research articles)on freesurfer documentation pages. Being new to the field and with very little image processing background i find it difficult to grasp the articles and other processing steps, so i am wondering is there a book on freesurfer (like books on SPM software and methods) which will take me step by step. Thanks in advance Regards venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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error in mri_glmfit-sim
by Roser Sala 09 Nov '09

09 Nov '09

Dear all, I am running a surface-based group analysis. When I try to run mri_glmfit-sim, I always get the following error: ERROR: you must supply --fwhm with --sim, even if it is 0 I get this error (which does not make any sense, since there is not fwhm info in the simulation) using both qdec-generated script and using command-line tools. The script that qdec generates is the following : /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir /home/eider/subjects/qdec/Untitled --sim perm 5000 2 perm.abs.2 --sim-sign abs --overwrite Does anyone know what could be happening?? Thanks - Roser -

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complex numbers overlay, colour wheel interpretation
by Andreas Schindler 09 Nov '09

09 Nov '09

Dear all I realised that freesurfer can handle overlays of complex numbers (e.g. as given by a fourier analyis) when they are split up in two separate volumes: one containing the real and the other containing the imaginary part of each voxel ("complex numbers" flag in the overlay configuration menu). It seems that freesurfer is able to read out the phase angle for each voxel and to depict different phases as different colours. However, unfortunately, when using the colour wheel, I haven't managed to figure out yet what colour corresponds to what phase (I assume the angles range from pi to -pi). Does anyone know how to interpret the colour wheel in that context? Many thanks, anyway best wishes Andreas

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4.5 and 4.4 longitudinal base creation error from mri_concatenate_lta
by Matt Erhart 09 Nov '09

09 Nov '09

Hello everyone, %% After running this command with v4.5 and v4.4: recon-all -base FREESURFERRECON_TEST_005_S_ 0221BASE45 -tp FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1 -tp FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1 -all -force %% I get this error: %%%%%%%%%% mri_concatenate_lta -invert1 FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1_to_FREESURFERRECON_TEST_005_S_0221BASE45.lta identity.nofile FREESURFERRECON_TEST_005_S_0221BASE45_to_FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1.lta invert the first LTA before applying it MatrixInverse: NULL input matrix! Read individual LTAs %%%%%%%%%% Any ideas on how to solve this? A side note for other troubleshooters: getting to this stage takes around 5 minutes with 2 subjects and around 90 minutes with 3. thanks! Matt

2 4

white matter mask
by Mehul Sampat 09 Nov '09

09 Nov '09

Hi Folks, I want to create a white matter mask (a volume in which all of the white matter voxels are 1 and 0 otherwise) For this, I am planning to use wmparc.mgz and then set the voxels with labels of wm-lh-? and wm-rh-? as 1. (here wm-lh-? represents labels such wm-lh-temporalpole, wh-lh-insula etc) >From wmparc.stats I found there are 35 such labels for each hemisphere. Is this the right way to create the white matter mask ? Thanks Mehul

2 2

corpus callosum bad segmentation...
by Gonzalo Rojas 09 Nov '09

09 Nov '09

Hi: I tried to segment a T1 volume of a 3 years old patient... It fails to segment the cortex in some specific regions, and the corpus callosum appears such as white matter... Why ?... Could I correct it ?... Sincerely -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Freesurfer November 2009