Freesurfer November 2012

freesurfer@nmr.mgh.harvard.edu

105 participants
177 discussions

Re: [Freesurfer] checking talairach.lta
by Douglas N Greve 05 Nov '12

05 Nov '12

I'm not sure that was the right thing to do. There should be two files: tkregister2 and tkregister2.bin. tkregister2 is just a script that calls tkregister2.bin after setting up some environment variables. Try keeping the original file name. doug On 11/05/2012 03:43 PM, Eric Cunningham wrote: > i am sure > there is one irregularity, namely that the '.bin' extension is absent > from our old file, so i renamed the new file without it (as > tkregister2) and moved the other one to tkregister2_backup > > the command i listed from previous threads was given to someone else > from our lab (and probably worked), so it is likely that the problem > is somewhere on our side, i was just hoping that it was known and > recognizable from the error > > > > On Mon, Nov 5, 2012 at 10:15 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > are you sure you are using the new version? > > > On 11/05/2012 02:38 PM, Eric Cunningham wrote: > > tried the new version, and it errored out at the same step > > ERROR: Option --lta-inv unknown > > thanks again for your help! > > On Mon, Nov 5, 2012 at 8:16 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Try using this version > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tkregister2.b… > copy it into $FREESURFER_HOME/bin (but make a back up of > the existing > tkregister2.bin first!) > doug > > On 11/02/2012 03:58 PM, Eric Cunningham wrote: > > Hi folks, > > In previous threads, the command provided to check the > talairach.lta is... > > tkregister2 --mov $FREESURFER_HOME/average/RB_all_2008-03-26.gca > \ --targ ../brainmask.mgz --lta-inv talairach.lta --reg > talairach.lta.reg.dat \ --surfs --s $subject > > > > When I try to run this command, I run into trouble with the > --lta-inv > > portion. (it is an unknown option). I am running version 5.1. > > Can anyone help? > > Thanks, > > -Eric > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] checking talairach.lta
by Douglas N Greve 05 Nov '12

05 Nov '12

are you sure you are using the new version? On 11/05/2012 02:38 PM, Eric Cunningham wrote: > tried the new version, and it errored out at the same step > > ERROR: Option --lta-inv unknown > > thanks again for your help! > > On Mon, Nov 5, 2012 at 8:16 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Try using this version > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tkregister2.b… > copy it into $FREESURFER_HOME/bin (but make a back up of the existing > tkregister2.bin first!) > doug > > On 11/02/2012 03:58 PM, Eric Cunningham wrote: > > Hi folks, > > In previous threads, the command provided to check the > talairach.lta is... > > tkregister2 --mov $FREESURFER_HOME/average/RB_all_2008-03-26.gca > \ --targ ../brainmask.mgz --lta-inv talairach.lta --reg > talairach.lta.reg.dat \ --surfs --s $subject > > > > When I try to run this command, I run into trouble with the > --lta-inv > > portion. (it is an unknown option). I am running version 5.1. > > Can anyone help? > > Thanks, > > -Eric > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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qcache error
by Berg, S.F. van den 05 Nov '12

05 Nov '12

Dear Freesurfer experts, I have got a problem with the qcache function. I have already runned 150 subjects with the recon-all command. Before i can work with the statistical program qdec i have to smooth the subjects. I want to smooth them with the command: recon-all -s <subject> -qcache. The command start to run but finished with errors. A overview of the terminal output is attached to this email in JPEG format. What is the problem in this case? further information about freesurfer version: recon-all -version: Id: recon-all, v 1.373 2011/03/15 00:43:47 mreuter Exp $ We run FreeSurfer-Linux-centos5_x86_64-dev-201110315 under Debian Squeeze. Thanks a lot, Stan van den Berg

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freeze old freesurfer distribution
by Bruehl, Hannah 05 Nov '12

05 Nov '12

Hi, I have a problem with the command for creating a frozen version of an old freesurfer distribution. When running the first step cp -Lr /usr/local/freesurfer/stable /path/to/yourdirectory/freesurfer I get the error that the -L flag is incompatible with the cp command: bruehh01% cp -Lr /Volumes/Macintosh\ HD/Applications/freesurfer/stable /Volumes/Macintosh\ HD/Applications/Freesurfer_4.5_BPD/freesurfer cp: the -H, -L, and -P options may not be specified with the -r option. can anyone help me with this? Thanks a lot! Hannah ...................................................................................................................................... Dr. Hannah Brühl Freie Universität Berlin Institut für Psychologie Arbeitsbereich Emotionspsychologie und affektive Neurowissenschaft Habelschwerdter Allee 45 — Raum JK 24/221h 14195 Berlin Tel.: +49 (0)30 838 571 68 ......................................................................................................................................

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(un)successfully extracted surfaces from FBIRN traveling subjects?
by Forrest Sheng Bao 05 Nov '12

05 Nov '12

Hi, Has anyone (un)successfully extracted surfaces from FBIRN traveling subjects? I just tried on the first 5 subjects of FBIRN traveling subjects Phase I. To every subject, the surfaces extracted from data sampled at Iowa (scans 1 and 2), Duke (scans 1 and 2) and UCI (scan 1) do not look well. Some of the hemispheres have parts of the other halves attached to it. Talairach transform also failed on these scans (I got the surface via -notal-check option). I tried using --mritotal for Talairach, but still no good. I did on both v5.0 and v5.1. However, on Standford2, UMN1 &2 and UNM1&2, the surfaces look very good. So I am wondering whether anyone out there has similar experience to mine, and whether they finally solved the problem. I am more interested in why Talairach failed on some scans and any solution other than manual alignment. Cheers, Forrest

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checking talairach.lta
by Eric Cunningham 05 Nov '12

05 Nov '12

Hi folks, In previous threads, the command provided to check the talairach.lta is... tkregister2 --mov $FREESURFER_HOME/average/RB_all_2008-03-26.gca \ --targ ../brainmask.mgz --lta-inv talairach.lta --reg talairach.lta.reg.dat \ --surfs --s $subject When I try to run this command, I run into trouble with the --lta-inv portion. (it is an unknown option). I am running version 5.1. Can anyone help? Thanks, -Eric

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Re: [Freesurfer] whole brain volume from ADNI UCSFFSL table
by Douglas N Greve 05 Nov '12

05 Nov '12

Sorry, I don't know anything about the UCSFFSL table. doug On 11/05/2012 11:41 AM, Zhiyong Xie wrote: > Hi Doug, > Thank you for your response. I did not find the single measurement for > Cortical Gray matter volume and Cortical white matter from UCSFFSL > table. looks like I need to add up all numbers for cortex regions and > plus subcortical regions you indicated and cerebellum. > Another thing that always confused me in UCSFFSL is hippocampus. In > the dictionary, it was reported as "Volume (WM Parcellation) of > LeftHippocampus/RightHippocampus". I did not find GM parcellation of > hippocampus. I do not know why hippocampus was classified as WM > parcellation. > Thank you for your help. > Sean > > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* freesurfer(a)nmr.mgh.harvard.edu > *Sent:* Monday, November 5, 2012 10:42 AM > *Subject:* Re: [Freesurfer] whole brain volume from ADNI UCSFFSL table > > Cortical Gray matter volume + Cortical white matter + subcortical gray > volume + cerebellum > subcortical gray is: > > Left_Thalamus > Right_Thalamus > Left_Thalamus_Proper > Right_Thalamus_Proper > Left_Caudate > Right_Caudate > Left_Putamen > Right_Putamen > Left_Pallidum > Right_Pallidum > Left_Hippocampus > Right_Hippocampus > Left_Amygdala > Right_Amygdala > Left_Accumbens_area > Right_Accumbens_area > Left_VentralDC > Right_VentralDC > > doug > > > On 11/02/2012 10:48 AM, Zhiyong Xie wrote: > > I knew this question has been asked before and it was suggested to use > > /SupraTentorial/ as the whole brain volume. I am working with ADNI > > data and cannot find this measurement from UCSFFSL table. As my > > understanding, UCSFFSL table was generated by Freesurfer 4.4. I was > > wondering which structures I should add up to get whole brain volume > > for comparison between AD, MCI, and normal people. > > Thanks > > Sean > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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whole brain volume from ADNI UCSFFSL table
by Zhiyong Xie 05 Nov '12

05 Nov '12

I knew this question has been asked before and it was suggested to use SupraTentorial as the whole brain volume. I am working with ADNI data and cannot find this measurement from UCSFFSL table. As my understanding, UCSFFSL table was generated by Freesurfer 4.4. I was wondering which structures I should add up to get whole brain volume for comparison between AD, MCI, and normal people. Thanks Sean

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Re: [Freesurfer] (no subject)
by Ryan 02 Nov '12

02 Nov '12

Doug, I tried running mri_glmfit-sim without the --bg flag and it finished in 10 minutes without any errors. This has never happened before, so I highly suspect these results. Do you know what could be wrong? In case you need it, the summary file output and terminal output are attached. -Ryan

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overlapping surfaces after running recon-all
by Deirdre O Shea 02 Nov '12

02 Nov '12

Hello FreeSurfer experts, I am having a lot of trouble with the surfaces on some of my subjects. The main problem is that I am getting an overlap of the surfaces which can be clearly seen in the coronal view (see attached for an example). This has happened with several subjects even using different commands. One of the commands I used which produced this result was "recon-all -autorecon2-cp -autorecon3 -noaseg subjid (subject)". The other command i used which also produced these results was "recon-all -autorecon-pial -noaseg subjid (subject)" I was using the -noaseg flag after I was deleting some of the segmentation voxels that extended out from the cerrebellum as this was also a common edit. This was specified in the tutorial. Is this the correct procedure? I'm thinking maybe the problem I'm seeing is related to this flag. I hope someone can help. Best Regards, Deirdre

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Freesurfer November 2012