Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30132 discussions

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. > > > > >

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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

2 3

.xdebug_tkmedit
by Paola Valsasina 15 Dec '10

15 Dec '10

Dear List, I installed version 5.0 of freesurfer on my Linux machine, when I tried to run tkmedit I got the attached error. Do you have any suggestion? Kind regards, Paola ----------------------------------------------------------------------------------- SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C'E' CURA SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org

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CUDA on Mac
by Martin Kavec 15 Dec '10

15 Dec '10

Hi all, I wonder if there are any plans to support CUDA on Mac platform. I see there are libraries available for the platform. Thanks a lot for feedback, Martin

2 1

Re: [Freesurfer] another recon-all error
by Thomas, Adam (NIH/NIMH) [E] 15 Dec '10

15 Dec '10

Bruce et al, Did you ever get to the bottom of Joakim's problem? I'm getting the same error. I checked the talairach and it looks fine. But for some reason mri_normalize can't find any peaks so T1.mgz comes out as all zeros. I just uploaded the subject to your anon FTP server.: ex03.2.tgz Thanks and let me know, -Adam On Thu, Nov 2010, Bruce Fischl wrote: Hi Joakim, you need to visualize the talairach.xfm applied to the orig.mgz in either tkregister2 or tkmedit to see if it is ok. mri_normalize clearly failed, and this is usually because of a failure in the talairach. It could also be that the nu intensity correction failed, so make sure to look at the nu.mgz as well. Or if you rather you can send us the nu.mgz and we can see what happened. cheers Bruce On Thu, 11 Nov 2010, Joakim Vinberg wrote: Bruce, I had quickly scanned the talairach.xfm, but I have to admit that I'm new to the process and wasn't sure what I was looking for. Here are the recon-all.log and talairach.xfm from this subject. Thank you for all the help! oakimJ -----Original Message----- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Wednesday, November 10, 2010 7:09 PM To: Joakim Vinberg Cc: <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] another recon-all error Did you check the talairach.xfm? Can you send us the recon-all.log file? On Nov 10, 2010, at 9:35 PM, "Joakim Vinberg" <jvinb...(a)omneuron.com> wrote: Sorry to add another! I ran recon-all on a subject of mine, and have recon-all exit with the error below. Based on the message, I examined both T1 and nu.mgz. T1.mgz is in fact totally emptyÿÿdefinitely not enough values of 110. Is this due to a specific error that I might be able to bypass, or will adding in WM control points fix things? Thanks in advance! Joakim //******************************************************** mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. Linux penguin 2.6.34.6-54.fc13.i686 #1 SMP Sun Sep 5 17:52:31 UTC 2010 i686 i686 i386 GNU/Linux recon-all -s 0142 exited with ERRORS at Wed Nov 10 16:55:08 PST 2010

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