Freesurfer April 2013

freesurfer@nmr.mgh.harvard.edu

131 participants
220 discussions

Re: [Freesurfer] Problems visualizing hippocampal subfields
by Erin Walsh 26 Apr '13

26 Apr '13

Hi Eugenio and Zeke, I attempted to enter the command line in again (re-copying/pasting) from the website. Perhaps I had entered in an error somewhere before because after 10+min, both volumes were able to load with the color maps. I will try replicating this to ensure it works. Apologies for my previous premature email-- I had tried the command a few times with the same errors, clearly I made an error somewhere. Just a few other questions: The "invalid drawable" message: Is that standard or is something truly awry with the command? It continues to appear. Does it normally take 10+min for the segmentation maps to appear? Many thanks, Erin -- Erin Walsh, Ph.D. Postdoctoral Research Associate University of Wisconsin-Madison Department of Psychiatry: Abercrombie Lab<http://www.psychiatry.wisc.edu/abercrombie/> 6001 Research Park Blvd. Madison, WI 53719 edubwalsh(a)gmail.com On Fri, Apr 26, 2013 at 3:08 PM, Erin Walsh <edubwalsh(a)gmail.com> wrote: > Thank you both! Much appreciated. > > Best, > > Erin > > > -- > Erin Walsh, Ph.D. > Postdoctoral Research Associate > University of Wisconsin-Madison > Department of Psychiatry: Abercrombie Lab<http://www.psychiatry.wisc.edu/abercrombie/> > 6001 Research Park Blvd. > Madison, WI 53719 > edubwalsh(a)gmail.com > > > On Fri, Apr 26, 2013 at 3:07 PM, Juan Eugenio Iglesias < > iglesias(a)nmr.mgh.harvard.edu> wrote: > >> The visualization Erin is shooting for actually weights the colors of >> each subfield by their probabilities, generating a nice, smooth, soft >> segmentation. >> Erin, Zeke is looking into the problem and will get back to you >> (hopefully) soon. >> Cheers, >> /Eugenio >> >> >> >> On Fri, 2013-04-26 at 16:03 -0400, Louis Nicholas Vinke wrote: >> > Hi Erin, >> > Try this command after cd into the subject's mri dir, treating the hippo >> > subfields as volumes. >> > >> > freeview nu.mgz posterior_Left-Hippocampus.mgz:colormap=heat >> > posterior_Right-Hippocampus.mgz:colormap=heat >> > >> > The labels are probability maps (Eugenio correct me if wrong) so >> > displaying with the FS look-up table makes them look like confetti. As >> a >> > heatmap makes more sense. >> > -Louis >> > >> > On Fri, 26 Apr 2013, Erin Walsh wrote: >> > >> > > Hi Freesurfers, >> > > >> > > I have been experiencing issues with visualizing the hippocampal >> subfields. >> > > I have attempted to try fixes I found in previous threads with no >> success. >> > > Hopefully someone here may have a solution. >> > > >> > > Thanks for any help! >> > > >> > > Erin >> > > >> > > >> > > >> > > Freesurfer Info: >> > > >> > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 >> > > Kernel info: Darwin 12.2.0 x86_64 >> > > >> > > >> > > Error Message: >> > > >> > > [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% freeview nu.mgz >> \ >> > > >> > > -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ >> > > >> > > -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ >> > > >> > > -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt >> > > >> > > 2013-04-26 14:19:16.237 freeview.bin[42704:f07] invalid drawable >> > > >> > > 2013-04-26 14:19:16.238 freeview.bin[42704:f07] invalid drawable >> > > >> > > 2013-04-26 14:19:16.250 freeview.bin[42704:f07] invalid drawable >> > > >> > > 2013-04-26 14:19:16.251 freeview.bin[42704:f07] invalid drawable >> > > >> > > 2013-04-26 14:19:16.262 freeview.bin[42704:f07] invalid drawable >> > > >> > > 2013-04-26 14:19:16.263 freeview.bin[42704:f07] invalid drawable >> > > >> > > 2013-04-26 14:19:16.274 freeview.bin[42704:f07] invalid drawable >> > > >> > > 2013-04-26 14:19:16.275 freeview.bin[42704:f07] invalid drawable >> > > >> > > QObject::connect: Connecting from QAbstractButton::toggled(bool) to >> COMPAT >> > > slot (QGroupBox::setShown(bool)) >> > > >> > > QObject::connect: Connecting from QAbstractButton::toggled(bool) to >> COMPAT >> > > slot (QGroupBox::setShown(bool)) >> > > >> > > [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% -p-labels >> > > posterior_left_* posterior_Left-Hippocampus.mgz \ >> > > >> > > -p-labels: Command not found. >> > > >> > > [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% -p-labels >> > > posterior_right_* posterior_Right-Hippocampus.mgz \ >> > > >> > > -p-labels: Command not found. >> > > >> > > [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% -p-prefix >> posterior_ >> > > -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt >> > > >> > > -p-prefix: Command not found. >> > > >> > > >> > > >> > > -- >> > > Erin Walsh, Ph.D. >> > > Postdoctoral Research Associate >> > > University of Wisconsin-Madison >> > > Department of Psychiatry: Abercrombie Lab >> > > 6001 Research Park Blvd. >> > > Madison, WI 53719 >> > > edubwalsh(a)gmail.com >> > > >> > > >> > _______________________________________________ Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> >> ------------------------------------------------------------------------------------- >> Juan Eugenio Iglesias, PhD >> http://www.jeiglesias.com >> iglesias(a)nmr.mgh.harvard.edu >> Athinoula A. Martinos Center for Biomedical Imaging >> Department of Radiology, MGH, Harvard Medical School >> 149 Thirteenth Street, Suite 2301 >> Charlestown, Massachusetts 2129 >> U.S.A. >> >> >> >> >> 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. >> > >

2 1

Problems visualizing hippocampal subfields
by Erin Walsh 26 Apr '13

26 Apr '13

Hi Freesurfers, I have been experiencing issues with visualizing the hippocampal subfields. I have attempted to try fixes I found in previous threads with no success. Hopefully someone here may have a solution. Thanks for any help! Erin Freesurfer Info: Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Kernel info: Darwin 12.2.0 x86_64 Error Message: [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt 2013-04-26 14:19:16.237 freeview.bin[42704:f07] invalid drawable 2013-04-26 14:19:16.238 freeview.bin[42704:f07] invalid drawable 2013-04-26 14:19:16.250 freeview.bin[42704:f07] invalid drawable 2013-04-26 14:19:16.251 freeview.bin[42704:f07] invalid drawable 2013-04-26 14:19:16.262 freeview.bin[42704:f07] invalid drawable 2013-04-26 14:19:16.263 freeview.bin[42704:f07] invalid drawable 2013-04-26 14:19:16.274 freeview.bin[42704:f07] invalid drawable 2013-04-26 14:19:16.275 freeview.bin[42704:f07] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels: Command not found. [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-labels: Command not found. [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt -p-prefix: Command not found. -- Erin Walsh, Ph.D. Postdoctoral Research Associate University of Wisconsin-Madison Department of Psychiatry: Abercrombie Lab<http://www.psychiatry.wisc.edu/abercrombie/> 6001 Research Park Blvd. Madison, WI 53719 edubwalsh(a)gmail.com

3 2

Alternate seed points in Tracula
by Sean Hatton 26 Apr '13

26 Apr '13

Hi all, Is it possible to use the Tracula bedpostx data to run Probtrackx with different seed points? For example: 1. Run all of Tracula on subject. 2. Extract seed masks from FS (eg seed superior temporal gurus to target anterior insula). 3. Run Probtrackx with the dbedpost data and masks in diffusion space. Is this feasible? I would get connection strength but how would I get FA, AD, RD etc? Should I correct for ICV? Or am I barking up the wrong tree? Sean Hatton Brain and Mind Research Institute University of Sydney

2 1

R: Re: R: Re: incomplete tracts
by stdp82＠virgilio.it 26 Apr '13

26 Apr '13

Hi Anastasia, I apologize but I do not find CVS template? Where it should be located? Thank you very much, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 9-apr-2013 17.50 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: incomplete tracts Hi Stefano - Did you try CVS for the inter-subject registration? It doesn't look like it from the configuration file. a.y On Tue, 9 Apr 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > yes, I tried.I'm attacking the last configuration file that I used. > > Thanks, > > > Stefano > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 9-apr-2013 1.42 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] incomplete tracts > > > What registration methods are you using for the intra-subject and > inter-subject registration? Have you tried the different options? > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > Yes, 5.2. Incomplete tracts are usually fmajor or cab. Rarely fminor. > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 5-apr-2013 18.57 > > A: <stdp82(a)virgilio.it> > > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] R: Re: R: Re: incomplete tracts > > > > > > What you say "again" you mean with 5.2? > > > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > Hi Anastasia, > > > yes, for some subject the low-b volume is in the end. > > > Some subjects have again incomplete tracts. > > > I'm attacking an example of configuration file that I'm using. > > > I hope that you can check it please. > > > > > > Thanks, > > > > > > > > > Stefano > > > > > > ----Messaggio originale---- > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > Data: 5-apr-2013 18.45 > > > A: <stdp82(a)virgilio.it> > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > > Ogg: Re: R: Re: [Freesurfer] incomplete tracts > > > > > > > > > Hi Stefano - In your case we determined that the ones that had the low-b > > > volume in the end didn't run correctly, right? In that case, I didn't > need > > > to see anything, you were going to try running 5.2. > > > > > > a.y > > > > > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > > > Hi Anastasia, > > > > could I send you the data of a subject that I don't run correctly? > > > > > > > > I still have some subjects with tracts incomplete and I do not know if > > it depends > > > from > > > > my analysis or whether the images are not good. > > > > > > > > Thanks, > > > > > > > > > > > > Stefano > > > > > > > > > > > > ----Messaggio originale---- > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > Data: 5-apr-2013 17.37 > > > > A: "Gerit Pfuhl"<gerit.pfuhl(a)gmail.com> > > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > > > Ogg: Re: [Freesurfer] incomplete tracts > > > > > > > > > > > > Hi Gerit - If it's not an issue with the gradient table but instead a > > > > tractography initialization issue, I strongly recommend running 5.2 > with > > > > bbregister for the registration (which is the default in 5.2 anyway). > > > > > > > > You can also upload an example data set with issues (include: dmri, > > > > dmri.bedpostX, dlabel, dpath, scripts) here for me to take a look: > > > > https://gate.nmr.mgh.harvard.edu/filedrop2/ > > > > > > > > Hope this helps, > > > > a.y > > > > > > > > On Fri, 5 Apr 2013, Gerit Pfuhl wrote: > > > > > > > > > Dear Anastasia, > > > > > > > > > > thanks for the help. There is also a line option in freeview. > However > > we still > > > have > > > > > brains with missing tracks, I rerun them with increasing the ncpts > and > > registering > > > > to > > > > > bbr (since that is default in Tracula 5.2.). We are reasonable > > confident that our > > > > bvel > > > > > and bvac are correct, since we have roughly 20 cases out of 90 > > processed brains > > > > where > > > > > there are no missing tracts. Further sometimes only one tract is > > missing, > > > sometimes > > > > it > > > > > is more severe. We could not find any correlation with recon-all > > problems or DTI > > > raw > > > > > data issues (all but one were without moving artefacts). Since we > are > > running > > > > bedpostx > > > > > outside of trac-all (i.e. trac-prep then bedpostx then trac-path) > > might it be an > > > > issue > > > > > that is solved with installing the 5.2. version? Would that run in > > freesurfer > > > 5.1.0? > > > > > I guess we need to change the dcmrirc files only a bit. > > > > > > > > > > Kind regards > > > > > Gerit Pfuhl > > > > > > > > > > > > > > > On 3 April 2013 16:59, Anastasia Yendiki > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > > > > > > > Hi Benjamin - I'd look in a coronal view to see if the lines > in > > the corpus > > > > > callosum follow the curvature of the corpus callosum, and in a > > sagittal > > > > > view to see if the lines in the cingulum follow the curvature > of > > the > > > > > cingulum. Does this make sense? > > > > > > > > > > a.y > > > > > > > > > > On Wed, 3 Apr 2013, Roschinski, Benjamin wrote: > > > > > > > > > > Dear Anastasia, > > > > > > > > > > we dislpayed dtifit_V1 as lines, overlaid on dtifit_FA because > > our > > > > > gradient table is wrong but I am not really sure how to > analyse > > > > > these informations. You wrote to Stefano the lines have to > point > > in > > > > > the right direction and that the eigenvectors are not pointing > > along > > > > > his corpus callosum. Can you give me a more detailed > description > > > > > what I have to do when I dislpay dtifit_V1 as lines, overlaid > on > > > > > dtifit_FA. > > > > > > > > > > Thanks and kind regards > > > > > Benjamin > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)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. > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > http://gerit-orientation.blogspot.com > > > > > http://team-arzgebirg.blogspot.com > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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. > > > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. > > > >_______________________________________________ Freesurfer mailing list Freesurfer(a)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.

2 1

Use our own training subjects?
by Susan Kuo 26 Apr '13

26 Apr '13

Hi Anastasia, We were viewing the arcuate fasiculus tract created by TRACULA, and noticed that the tract did not reach Broca's area. While there exists literature that now challenges this neuroanatomical convention, I would like to investigate the possibility of creating and inputting on our own training subjects as priors. Do you know if we can try this? Thank you! -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear*

2 1

Tracula 5.2.0 -path step segmentation fault
by Gerit Pfuhl 26 Apr '13

26 Apr '13

Dear Freesurfer experts, Running tracula in freesurfer 5.2.0 gave me now an unsual errror. No problems in the trac-prep and trac-bedp step but suddenly segmentation fault in trac-path. The other threads state it is a problem in a previous step. However, the subject was processed fine in version 5.1.0 though some tracts were incomplete - that is why we try the new better algorithm. I found no difference in the dmri and dmribedpostx folders (a few more files in xfms compared to using tracula 5.1.0 version). I used the defaults in the dmrirc file and attach the log file. Kind regards Gerit Pfuhl

2 1

Re: [Freesurfer] Problem running Tracula longitudinal analysis
by Anastasia Yendiki 26 Apr '13

26 Apr '13

Hi Dylan - Thanks for your patience. There was a small scripting bug that was causing trac-all in longitudinal mode not to process the command line properly on some systems. Can you please copy the two modified scripts I'm attaching to your $FREESURFER_HOME/bin, overwriting the existing versions? Please let me know if that fixes the error, and if so I'll post them to the wiki as an update for anyone else who wants to run longitudinal. Thanks, a.y On Tue, 9 Apr 2013, Dylan Nielson wrote: > This should be what you need, Let me know if I've sent the wrong one. > > > On Tue, Apr 9, 2013 at 11:30 AM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Dylan - Can you send your trac-all.log file? (When the baselist is > included in the dmrirc, otherwise you're just running the cross-sectional tractography.) > > Thanks, > a.y > > On Mon, 8 Apr 2013, Dylan Nielson wrote: > > I'm running CentOS 6.4. I don't know if it matters, but I tried running the > command from both bash and tcsh and they both give an error. Also, I did the > bedpost outside of freesurfer and then copied the outputs from that into the > freesurfer directories where they're supposed to go. The dcmric file will > run if I take out the baselist portion. > Any ideas you have would be great. > > Thanks, > > Dylan > > > On Mon, Apr 8, 2013 at 8:04 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Dylan - First of all kudos for being a brave early adopter :) > The only thing wrong with the dmrirc that I see is that there > can be only one bvecfile and bvalfile, not one per time point > (it's assumed that you used the same protocol for all time > points). > > That said, I don't think that's what's causing the error. What > operating system and version are you running this on? > > a.y > > On Sat, 6 Apr 2013, Dylan Nielson wrote: > > I am trying to run Tracula on a single subject with > two time points. I get the following Error > below. I suspect it is because I am not setting my > dmrirc file up correctly, but I cannot > figure out what the error is. I've copied my dmrirc > file below as well. > > Thanks, > > Dylan > > Command: > trac-all -prep -nocorr -nointra -c > dmrirc.long.RP0603 > > Error: > > trac-preproc -c > > /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/dmrirc.local > -log > > /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.log > -cmd > > /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.cmd > ; trac-preproc -c > > /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/dmrirc.local > -log > > /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.log > -cmd > > /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.cmd > ; trac-preproc -c > /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/dmrirc.local > -log > /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.log > -cmd > /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.cmd > ; > ERROR: flag ; unrecognized > -c > > /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/dmrirc.local > -log > > /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.log > -cmd > > /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.cmd > ; trac-preproc -c > > /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/dmrirc.local > -log > > /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.log > -cmd > > /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.cmd > ; trac-preproc -c > /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/dmrirc.local > -log > /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.log > -cmd > /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.cmd > ; > > dmrirc.long > setenv SUBJECTS_DIR ~/fmri/RP0629_3T/freesurfer > set dtroot = ~/fmri/RP0629_3T/freesurfer > set subjlist = ( tp1002.long.002 \ > tp2002.long.002 ) > set baselist = ( 002 002 ) > set dcmroot = ~/fmri/RP0629_3T/freesurfer/ > set dcmlist = ( tp1002.long.002/dmri/dwi.nii.gz \ > tp2002.long.002/dmri/dwi.nii.gz ) > set bvecfile = ( tp1002.long.002/dmri/bvec \ > tp2002.long.002/dmri/bvec ) > set bvalfile = ( tp1002.long.002/dmri/bval \ > tp2002.long.002/dmri/bval ) > set dob0 = 0 > set doeddy = 0 > set thrbet = 0.5 > set doregflt = 0 > set doregbbr = 1 > set doregmni = 0 > set doregcvs = 1 > set cvstemp = cvs_avg35 > set cvstempdir = $FREESURFER_HOME/subjects > set usemaskanat = 1 > set pathlist = ( lh.cst_AS rh.cst_AS \ > lh.unc_AS \ > lh.ilf_AS \ > fmajor_PP fminor_PP \ > lh.atr_PP rh.atr_PP \ > lh.ccg_PP rh.ccg_PP \ > lh.cab_PP rh.cab_PP \ > lh.slfp_PP rh.slfp_PP \ > lh.slft_PP rh.slft_PP ) > set ncpts = (6 6 5 5 7 7 5 5 5 5 4 4 5 5 5 5) > set trainfile = > $FREESURFER_HOME/trctrain/trainlist.txt > set nstick = 2 > set nburnin = 200 > set nsample = 7500 > set nkeep = 5 > set reinit = 0 > > > > > 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

a question
by limeilingcheng 26 Apr '13

26 Apr '13

Hi all, Now I got some results by freesurfer, finally I selected two vertexs which the coordinate values were(Talx=-40.5, Taly= -14.5,Talz=-12.7 and Tal x=55.1, Tal y=-23.9, Tal z=-1.8 ), the corresponding regions reported by freesurfer were left superiortemporal and right superiortemporal. In the following step, I want to make the left and right superiortemporal as ROIs and observe the functional connectivity between the ROIs and the voxels in the whol brain. However, it is difficult for me to understand how to get the ROIs I want based on Harvard-Oxford atlas(?) according to my coordinate values from freesurfer,especially it was Talairach index, and if we get the transformed coordinate values in the Harvard-Oxford atlas, should I make the corresponding whole region as the ROI? Regards, Meiling

1 0

asegstats2table error depending on subject sorting
by Andreas Berger 26 Apr '13

26 Apr '13

Hi Surfers, as of version 5.2, i'm getting an error using asegstats2table, depending on how i sort the subjects: andreas@psy058:~$ asegstats2table --subjects $(ls $SUBJECTS_DIR | sort -t _ -k 1 -nk 2) -t segstats.csv --skip -d comma SUBJECTS_DIR : /mnt/raid/freesurfer/subjects Parsing the .stats files Skipping /mnt/raid/freesurfer/subjects/fsaverage/stats/aseg.stats Skipping /mnt/raid/freesurfer/subjects/lh.EC_average/stats/aseg.stats Skipping /mnt/raid/freesurfer/subjects/qdec/stats/aseg.stats Skipping /mnt/raid/freesurfer/subjects/rh.EC_average/stats/aseg.stats Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 553, in <module> if(nmeasures != nmeasures0 and not options.common_flag and not options.all_flag): NameError: name 'nmeasures0' is not defined i don't get that error if i either: 1) remove the non-subjects (fsaverage, qdec, etc..) from the list, or: 2) do not sort the list like i do the subjects list is attached, sorted the way it produces the error greetings, Andreas

2 2

Re: [Freesurfer] convert labels to volumetric masks
by limengsecret 25 Apr '13

25 Apr '13

Hi Doug, Thanks for your reply. The mask created is used to register with the normalized functional data and to define the roi, so could I run the following command? tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg ./register.dat/ and the func.nii has been normalized (sub.nii) to the MNI space. The .w file I download from http://ltl.tkk.fi/wiki/Atlas, indicates the maximum probability map. Best wishes, Meng Dear FreeSurfers, I want to convert cortical labels to volumetric masks, and I run the following commands: 1. /tkregister2 -mov sub/mri/rawavg.mgz -noedit -s sub -regheader -reg ./register.dat/ 2. /mri_label2vol -label ./lh.entorhinal.label -temp sub/mri/rawavg.mgz -subject sub -hemi lh -o sub_lh_entorhinal.nii.gz -proj frac 0 1 .1 -fillthresh .3 -reg ../mri/register.dat/ if I do not run the recon-all command, could I change the rawavg.mgz to sub.nii (original data)? What is sub.nii? The second problem is that when I convert the annotation file to volumetric mask, whether I should convert the file to labels using mri_annotation2label first, then run the commands as decribed above, or there is a way that could convert the annotation file to volumetric mask directly? You can use the same label2vol command above but spec --annot instead of --label The last problem is that how to convert the .curv file and .w file to volumetic mask? mri_surf2vol should work for the curv file. Why do you have a .w file? BTW, for our standard annotations (aparc and aparc.a2009s) you will probably be happier with the results if you use mri_label2vol with --seg aparc+aseg.mgz or --seg aparc.a2009s+aseg.mgz. Otherwise, there are some holes that are created if you use the surface labels. doug

1 0

← Newer
1
2
3
4
5
6
7
...
22
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer April 2013