Freesurfer December 2010

freesurfer@nmr.mgh.harvard.edu

92 participants
128 discussions

Cortical Classifier for PALS
by Lena Palaniyappan 18 Dec '10

18 Dec '10

I want to use the annot file for lobar areas in fsaverage to be mapped onto all of my subjects. As I don't want to disassemble the annot to single labels but generate lobar.annot for all subjects, I intend to use mris_ca_label -l fsaverage/label/lh.PALS_B12_Lobes.annot <subjid> lh lh.sphere.reg <classifier> subjid/label/lh.PALS_Lobes.annot For this purpose. What cortical classifier file should I use to map the different PALS atlases (at least - the two of them : Brodmann and Lobes) Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

2 4

(no subject)
by Giovanni Rodriguez 17 Dec '10

17 Dec '10

To Whom It May Concern: My name is Giovanni Rodriguez, I am a high school student working at the University of Miami in a research lab. My lab professor told me to work through the basics on my own and to download the tutorial and dataset. Is there anyway that I could find a dumb proof, step by step manual on how to download and work through Freesurfer? Thank you in advance, Gio

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Re: [Freesurfer] Difficulty running FreeSurfer
by Nisser ali umar 17 Dec '10

17 Dec '10

2 1

Trying to run recon-all on old raw data
by Lisa F. Akiyama 17 Dec '10

17 Dec '10

Hello FreeSurfer experts, I am trying to run recon-all on old (back from late 1990's) raw MRI data. Each slice is in a raw format. When I try to execute recon-all, I get the error shown below: todd:~$ recon-all -subjid A_H -i > $SUBJECTS_DIR/adults_jp/A_H/slices/HA970313a1997031316500756 Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux neptune-ubuntu 2.6.35-23-generic #41-Ubuntu SMP Wed Nov 24 11:55:36 > UTC 2010 x86_64 GNU/Linux /usr/local/freesurfer/subjects/A_H > mri_convert > /usr/local/freesurfer/subjects/adults_jp/A_H/slices/HA970313a1997031316500756 > /usr/local/freesurfer/subjects/A_H/mri/orig/001.mgz > mri_convert > /usr/local/freesurfer/subjects/adults_jp/A_H/slices/HA970313a1997031316500756 > /usr/local/freesurfer/subjects/A_H/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from > /usr/local/freesurfer/subjects/adults_jp/A_H/slices/HA970313a1997031316500756... Getting Series No INFO: Found 136 files in /usr/local/freesurfer/subjects/adults_jp/A_H/slices INFO: Scanning for Series Number 32664 Scanning Directory INFO: found 0 files in series ERROR: could not find any files (SeriesList==NULL) Linux neptune-ubuntu 2.6.35-23-generic #41-Ubuntu SMP Wed Nov 24 11:55:36 > UTC 2010 x86_64 GNU/Linux > recon-all -s A_H exited with ERRORS at Mon Dec 13 14:34:21 PST 2010 Does anyone know how to resolve this issue? Thank you. Best, Lisa ______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington E-mail: lrisa87(a)uw.edu P Please consider the environment before printing this e-mail.

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Re: [Freesurfer] Difficulty running FreeSurfer
by Nisser ali umar 16 Dec '10

16 Dec '10

2 1

How to adjust cortical thickness/area/volume measures from autorecon3
by Liukarl 16 Dec '10

16 Dec '10

Hello, Freesurfer experts: I found to report subcortical volumetric measure, ie, the volume of amygdale, people tend to use icv as a control variable. Is there any corresponding measure to correct the cortical thickness/area/volume results from autorecon3. Because we have priori hypothesis of hemisphere dichotomy of cortical structures, we need some control variable for each hemisphere. We want to use an overall measure for each hemisphere as a control variable. For example, to measure the group differences on rh_paracentral_thickness, we will use the rh_whole_thickness as a contral variable (which is the sum of the thickness measures of all the ROIs in the right hemisphere produced by Freesurfer). Similarly, to measure the group differences on rh_paracentral_area and rh_paracentral_volume, we will use the rh_whole_area and rh_whole_area as a contral variable respectively. Is this a valid approach to report our results? Thanks a lot! Karl

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WM parcelleted boundary
by Ingalhalikar, Madhura 15 Dec '10

15 Dec '10

Hi, Is there a way to get the cortical parcellations projected onto the WM boundary? I need to seed the boundary of the cortical ROI ( in WM) for fiber tracking. Please let me know, Thank you, Madhura The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by e-mail, and delete the original message.

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Re: [Freesurfer] Difficulty running FreeSurfer
by Bruce Fischl 15 Dec '10

15 Dec '10

Hi Thomas, you need to create that file. cheers Bruce On Wed, 15 Dec 2010, Obisesan, Thomas O. wrote: > Thanks Bruce, > > Unfortunately, we are unable to locate any such file. Any directives on how to locate the file will be helpful. Additionally, we are unable to paste into the Xterminal. > > Thanks > Thomas Obisesan > > ----- Original Message ----- > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Nisser ali umar <nisser.au(a)usa.net> > Cc: Freesurfer(a)nmr.mgh.harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>; ryorrickster(a)gmail.com <ryorrickster(a)gmail.com>; Obisesan, Thomas O. > Sent: Wed Dec 15 20:11:05 2010 > Subject: Re: [Freesurfer] Difficulty running FreeSurfer > > Hi Nisser, > > put it in a file named $FREESURFER_HOME/.license > > > cheers > Bruce > > On Thu, 16 Dec 2010, Nisser ali > umar wrote: > >> Hi, >> >> We installed freesurfer on a mac computer but could not find where to >> paste the license code, thus have difficulty getting the freesurfer >> running. >> >> Can anyone help, please. >> >> Nisser >> >> >> >> >> >> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > > >

1 0

Difficulty running FreeSurfer
by Nisser ali umar 15 Dec '10

15 Dec '10

3 2

mri_convert float to uchar
by Yang Liu 15 Dec '10

15 Dec '10

Hello all, I am converting one .mgz file to another like this: mri_convert -i a.mgz -o conformed_a.mgz --conform The data type of a.mgz is float. After the conversion, The conformed_a.mgz is uchar. However, I found that the places surrounding the brain which have 0 grayscale values in the a.mgz are having grayscale value 108 in the confored_a.mgz. This makes the conformed_a.mgz very whitish compared to the original one. Is there a way to make the float 0 to a uchar 0? Thanks. Yang

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Freesurfer December 2010