Freesurfer

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30132 discussions

error using recon-all function
by Ryan Hutten 29 Jun '11

29 Jun '11

Hi, I am currently trying to use the recon-all function. It works fine on an older computer, but my group is attempting to get freesurfer up and running on a newer computer. The subject data is located in a folder called 2645166 as shown in the following command. When I run the command: recon-all -s 2645166 -all I get the following error after the script runs for about a minute: ERROR: avi2talxfm failed, see transforms/talairach_avi.log Linux dell3 2.6.35.6-45.fc14.x86_64 #1 SMP Mon Oct 18 23:57:44 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux The output of your bugr script gives: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: Fedora release 14 (Laughlin) Kernel info: Linux 2.6.35.6-45.fc14.x86_64 x86_64 A brief internet search found nothing regarding this avi2talxfm function. Any suggestions and/or help would be greatly appreciated. Thanks,

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Re: [Freesurfer] Freesurfer Digest, Vol 88, Issue 86
by Antonella Kis 29 Jun '11

29 Jun '11

Good afternoon Bruce, I am not sure what video card I am using (and I am not sure how to do the updating for my video driver) but I could see these surfaces on the same computer while using an old Freesurfer version V.5.0. I saved this old version on my computer under freesurfer_backup and I re-installed the new version V.5.1.0. (my FREESURFER_HOME directory is directed to the new version v.5.1.0). I wonder if this maybe the reason or there maybe some problem with my insatllation? Many thanks for helping. Antonella ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of freesurfer-request(a)nmr.mgh.harvard.edu [freesurfer-request(a)nmr.mgh.harvard.edu] Sent: Wednesday, June 29, 2011 12:00 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 88, Issue 86 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Error with Tkmedit (Bruce Fischl) ---------------------------------------------------------------------- Message: 1 Date: Wed, 29 Jun 2011 10:49:56 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error with Tkmedit To: Antonella Kis <atorok9(a)yahoo.com> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <alpine.LRH.2.00.1106291049290.8015(a)gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-15" Hi Antonella what video card are you using? Did you try updating your video driver? cheers Bruce On Wed, 29 Jun 2011, Antonella Kis wrote: > > Good morning, > > Thank you very much Bruce. I attached the tiff file and I am posting my message again on the list: > > I am having problem with tksurfer. > > When I run: > > ?tksurfer lh inflated > > for NPI002, the image is looking totally weird. I don't understand why I cannot get the correct lh inflated since there is no error while running tksurfer. > > ?I attached the tiff? image for the lh inflated for the NPI002 case after running tksurfer. I get similar image for the bert's data included as a freesurfer sample data. > > > Thank you! > Antonella > > > ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 88, Issue 86 ****************************************** 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. ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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Re: [Freesurfer] Error with Tkmedit
by Bruce Fischl 29 Jun '11

29 Jun '11

Hi Antonella what video card are you using? Did you try updating your video driver? cheers Bruce On Wed, 29 Jun 2011, Antonella Kis wrote: > > Good morning, > > Thank you very much Bruce. I attached the tiff file and I am posting my message again on the list: > > I am having problem with tksurfer. > > When I run: > > tksurfer lh inflated > > for NPI002, the image is looking totally weird. I don't understand why I cannot get the correct lh inflated since there is no error while running tksurfer. > > I attached the tiff image for the lh inflated for the NPI002 case after running tksurfer. I get similar image for the bert's data included as a freesurfer sample data. > > > Thank you! > Antonella > > >

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registration with Melodic
by Kat Mott 29 Jun '11

29 Jun '11

Hi all, I have manually registered fMRI data that I want to run ICA on, and I want Melodic to use my register.dat file, not re-register the data using its own algorithm. Since there doesn't seem to be any way to use the register.dat file as an input, I've been trying to figure out a way to apply the registration info to the .nii file and then simply uncheck the registration options in Melodic. I used a bit of code I found in the forum archives to try this, which created, using the f.nii and register.dat file, a file called f.anat.nii. But when I tried to use this as the 4D input for Melodic I got the error 'Child process exited abnormally.' I used the following to perform the transformation into f.anat.nii: mri_vol2vol --mov f.nii --reg register.dat --fstarg --o f.anat.nii Any thoughts on how to create an input that Melodic will accept so that it will use my registration? Thanks much, Kat

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MRI volume padding in pipeline
by Lukas Fiederer 29 Jun '11

29 Jun '11

Good day everyone, I received a Freesurfer processed MRI volume from a college and would like to compare it to the unprocessed data. Alas Freesurfer padded the MRI volume from [384 384 256] to [385 385 385]. I would like to revert this padding! Can someone please be kind enough to tell me in which way the pads are added, ie. how much is added on each side of each dimension. Thanks a lot, Lukas

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MRI_Convert error on recon-all process
by Jordi Casals 29 Jun '11

29 Jun '11

Hello, My name is Jordi Casals. I've been trying to process some subjects with recon-all, but the procees is giving me this error: SUBJECT DFF_082 DATE Tue Jun 28 16:58:40 CEST 2011 USER neuro HOST td547.pic.es PROCESSOR x86_64 OS Linux Linux td547.pic.es 2.6.18-238.9.1.el5 #1 SMP Tue Apr 12 18:53:46 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.313.2.6 2010/08/04 15:50:56 nicks Exp $ /SOFTWR/freesurfer5/bin/recon-all PWD $PATH/DFF_082 CMD mri_convert /DICOM/T13D/DFF_082/DFF_082_0002 $PATH/DFF_082/mri/orig/001.mgz and the recon-all log have the following lines: mri_convert /DICOM/T13D/DFF_082/DFF_082_0002 $PATH/DFF_082/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /DICOM/T13D/DFF_082/DFF_082_0002... Starting DICOMRead2() dcmfile = /DICOM/T13D/DFF_082/DFF_082_0002 dcmdir = /DICOM/T13D/DFF_082 WARNING: tag ImageNumber not found WARNING: tag image orientation not found Ref Series No = 301 ERROR: bits = 0 not supported. Send email to freesurfer(a)nmr.mgh.harvard.edu Linux td547.pic.es 2.6.18-238.9.1.el5 #1 SMP Tue Apr 12 18:53:46 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s DFF_082 exited with ERRORS at Tue Jun 28 16:58:40 CEST 2011 I searched for possible solutions but some of them I don't really understand what I really have to do and the other solutions didn't seem to work. I don't know how to correct the error to reach the complete execution of the process. If someone can help me or guide me to the solution, I would be very grateful. Thank you, Jordi.

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Recon-all with mris_fix_topology error
by Jordi Casals 29 Jun '11

29 Jun '11

Hello FreeSurfer community, I am Jordi Casals, from Barcelona. After few days trying to process a set of modificactions done to a subject (pial, white matter and control points), I still have this error, about mris_fix_topology. I don't know where is the problem, because I have done a lot of subjects in the same way as these one and the other two that give me this error. SUBJECT SRN_005 DATE Wed Jun 22 00:58:31 CEST 2011 USER neuro HOST td560.pic.es PROCESSOR x86_64 OS Linux Linux td560.pic.es 2.6.18-238.9.1.el5 #1 SMP Tue Apr 12 18:53:46 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.133.2.43 2009/04/22 22:34:03 nicks Exp $ /SOFTWR/freesurfer/bin/recon-all PWD $PATH/SRN_005/scripts CMD mris_fix_topology -mgz -sphere qsphere.nofix -ga SRN_005 rh It would be be really great if someone can help me or give me some guides to understand a little bit more the problem and to reach a proper execution. Thank you again, Jordi.

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Tracula question: group analysis
by Maryam Moteabbed 28 Jun '11

28 Jun '11

Hello Tracula Developers & Users, I can follow how to use the diffusion measures from pathstats.overall.txt for each subject to run a group analysis on the tracts. On the other hand I noticed there is also the pathstats.byvoxel.txt which contains various diffusion measures in each voxel along the highest probability path. What are your suggested steps for analyzing this text file for group comparison? I am guessing developers had an analysis method in mind when they decided to print this file out. Thank you in advance for your help. Best, Mary

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Re: [Freesurfer] your mail
by Bruce Fischl 28 Jun '11

28 Jun '11

Hi Antonella, gzip doesn't recognize your file. Can you just send us a tif? Bruce On Tue, 28 Jun 2011, Antonella Kis wrote: > > Once again thanks Bruce. I am posting this message also to the list: > > I am having problem with tksurfer. > > When I run: > > tksurfer lh inflated > > for the Freesurfer data sample called bert, the image is looking totally weird. I don't understand why I cannot get the correct lh inflated since there is no error while > running tksurfer. > > I attached the archive image of the lh inflated for the bert case after running tksurfer. > > > >

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mri_glmfit-sim problem...
by Joe Andreano 28 Jun '11

28 Jun '11

Hi All, I tried using glmfit-sim to for multiple comparison correction on some previously analyzed data, and I've run into an error I don't understand: Here's the command I used: mri_glmfit-sim --glmdir tal.wrfx.arousal_v_valence_TP0 --cache 1.3 pos This generated the following error: ERROR: cannot find /usr/local/freesurfer/stable5_1_0/average/mult-comp-cor///cortex/fwhm12/pos/th13/mc-z.csd I checked the location mentioned in the message, and the mc-z.csd file is indeed there. Does anyone know what this means? Thanks, Joe _________________________________ Joseph M. Andreano, PhD Research Fellow Interdisciplinary Affective Science Lab Massachusetts General Hospital _________________________________

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