Siti, can you give us the full command-line (without the variables) and the full terminal output?
doug Siti Hajar wrote: > When I ran this command, " mri_segstats --seg > "$fsaveragesurfpath"/"$hemi".fsaverage."$hemi"_"$roi"_"$subj".mgh --in > "$hemi".thickness.fsaverage.mgh --sum > segstats-"$hemi"_"$roi"_"$subj".txt, this kind of output came out > "mghRead(/usr/local/freesurfer/subjects/100905lsy/surf/lh.thickness.fsaverage.mgh, > > -1): could not open file--> which indicated that there was no > lh.thickness.fsaverage.mgh created. Well, basically, when I ran > recon-all, lh.thickness.fsaverage.mgh should be created, but it > wasn't. So, again with my question,is this situation happened due to > the new freesurfer software that I installed or was it caused by other > source? The skull strip result was ok > > > *From:* "freesurfer-requ...@nmr.mgh.harvard.edu" > <freesurfer-requ...@nmr.mgh.harvard.edu> > *To:* freesurfer@nmr.mgh.harvard.edu > *Sent:* Mon, September 20, 2010 9:49:16 PM > *Subject:* Freesurfer Digest, Vol 79, Issue 32 > > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@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-requ...@nmr.mgh.harvard.edu > <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > <mailto:freesurfer-ow...@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: mri_label2volume issues (Michael Waskom) > 2. Generating a 'non-zero' group mask (Marco Loggia, PhD) > 3. Re: recon-all quality control checks on large numbers of > subjects (Nick Schmansky) > 4. lh.thickness.fsaverage (Siti Hajar) > 5. Re: lh.thickness.fsaverage (Douglas Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 17 Sep 2010 11:04:00 -0400 > From: Michael Waskom <mwas...@mit.edu <mailto:mwas...@mit.edu>> > Subject: Re: [Freesurfer] mri_label2volume issues > To: Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <aanlkti=5znihxybqu0wwf-ysjn6opoqk2bfuf2_ii...@mail.gmail.com > <mailto:5znihxybqu0wwf-ysjn6opoqk2bfuf2_ii...@mail.gmail.com>> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Prapti, > > Basically, you just need to have a label file that you can turn into a > lh.your_annot_name.annot (assuming your actual ROI is in the right > hemisphere), so that mri_label2annot runs properly. > > The easiest thing to do would be to rename any old label you have in > your subject's label directory to lh.dummy.label, and then create an > annotation from that label with mri_label2annot. Then run > mris_aparc2aseg as you tried to do before, which will create a volume > that has 0's everywhere except in the area where your actual and dummy > labels were projected. Figure out the voxel values for the ROI you > want (using Freeview or tkmedit), and then run: > > mri_binarize --i your_annot_name+aseg.mgz --match <that voxel value> > --o you_roi_name.mgz > > Which will have 1s where your ROI is and 0s everywhere else. > > Best, > Mike > > -------Original Message------- > > Hi Doug, > Thanks for the reply. I am sorry, I am a bit confused about what you > mean by creating a dummy label. I am also not sure at which step I need > to do this. > > As I understand it, I use mri_label2annot to transform my label into a > annotation file and this will be separate for the two hemispheres. Do I > then edit these files ? where exactly do I use mri_binarize? > > Thanks, > > Prapti > > -----Original Message----- > From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>] > Sent: Friday, 17 September 2010 12:44 AM > To: Prapti Gautam > Cc: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mri_label2volume issues > > Right, I see, mri_aparc2aseg is hard-coded to expect both lh and rh. The > > easiest thing is to make a dummy label for the other hemisphere. In the > final segmentation, left hemisphere will have an index of > 1000+something, the right will have 2000+something. You can then use > mri_binarize with --match create a new binary volume with just your > hemisphere. > > doug > > Prapti Gautam wrote: > > Hi Doug, > > > > Thanks for the reply. I have tried using the method you've suggested, > > however, I'm stuck because mri_label2annot which I use to turn my > label > > into a annot file only works in one hemisphere while mri_aparc2aseg > > works for the whole brain. Do you know a work around for this? > > > > Can I merge the annot files created from each hemisphere so that I can > > pass it to mri_aparc2aseg? > > > > > > Thanks, > > > > Prapti > > > > > > > > > ------------------------------ > > Message: 2 > Date: Fri, 17 Sep 2010 11:38:22 -0400 > From: "Marco Loggia, PhD" <ma...@nmr.mgh.harvard.edu > <mailto:ma...@nmr.mgh.harvard.edu>> > Subject: [Freesurfer] Generating a 'non-zero' group mask > To: <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: <5ea6cf4fa3914bc49d4cc51bd03a8...@marcowork> > Content-Type: text/plain; charset="us-ascii" > > Dear all, > > > > I am performing surface analyses on ASL CBF maps. As these maps do not > cover > the whole brain, and some masks have larger brain coverage than others, I > would need to create a binary surface mask (in the fsaverage space) which > would zero out the vertices where at least one of my subjects have a zero > value. This map would then be used to spatially limit my statistical > analyses in mri_glmfit. > > > > Any suggestions? > > > > Thanks a lot, > > > > Marco > > > > > _____________________ > > > > Marco L. Loggia, PhD > > Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital > > Harvard Medical School > > > > CNY Building 120, suite 101E > > Charlestown, Massachusetts 02129 > > Phone: (617) 643-7267 > > Fax: (617) 643-7340 ma...@nmr.mgh.harvard.edu > <mailto:ma...@nmr.mgh.harvard.edu> > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20100917/e53967b7/attachment-0001.html > > > > ------------------------------ > > Message: 3 > Date: Fri, 17 Sep 2010 18:41:09 -0400 > From: Nick Schmansky <ni...@nmr.mgh.harvard.edu > <mailto:ni...@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] recon-all quality control checks on large > numbers of subjects > To: Pradeep <tprad...@gmail.com <mailto:tprad...@gmail.com>>, > Freesurfer Mailing List > <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Cc: kewei chen <keweichen7...@gmail.com <mailto:keweichen7...@gmail.com>> > Message-ID: <1284763269.543.5.ca...@terrier.nmr.mgh.harvard.edu > <mailto:1284763269.543.5.ca...@terrier.nmr.mgh.harvard.edu>> > Content-Type: text/plain > > consult this page: > http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems > > typically the problem is resolved by upgrading the nvidia driver > (assuming you have such a graphics card). > > n. > > On Fri, 2010-09-17 at 15:17 -0700, Pradeep wrote: > > Hello Nick, > > > > The data_check program works after some minor fixes. > > > > I now a have problem with tksurfer on our server > > > > The recon-all step ran with out any errors > > > > But > > tksurfer AD_C165 lh smoothwm > > displays only a part of the image and dose not give any error > > messages. > > > > Machine Details: x86_64 GNU/Linux > > FreeSurefer Version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 > > > > So i downloaded the images to another computer and the display is good > > here. > > > > Machine Details: i686 GNU/Linux > > FreeSurfer Version: freesurfer-Linux-centos4-stable-pub-v5.0.0 > > > > > > Any suggestions on this would be greately appreciated. > > > > Thanks, > > Pradeep > > > > > > > > > > On Thu, Sep 16, 2010 at 5:32 PM, Pradeep <tprad...@gmail.com > <mailto:tprad...@gmail.com>> wrote: > > Thanks for letting us know. > > > > Is there any other way to do the QA in batch ? > > > > Thanks, > > Pradeep > > > > On Thu, Sep 16, 2010 at 3:52 PM, Nick Schmansky > > > > <ni...@nmr.mgh.harvard.edu > <mailto:ni...@nmr.mgh.harvard.edu>> wrote: > > > sorry, this is no longer supported. it was created by an ra > > who left > > > the center a few years ago. i suppose i should have > > mentioned that in > > > my original email. > > > > > > n. > > > > > > On Thu, 2010-09-16 at 15:51 -0700, Pradeep wrote: > > >> Hell Nick, > > >> > > >> Looks like the recon_checker has some problems to fix > > >> > > >> Below is my log file. > > >> > > >> ############ > > >> surf/rh.sphere surf/rh.sphere.reg surf/rh.lh.sphere.reg > > >> surf/rh.avg_curv label/rh.aparc.annot stats/rh.aparc.stats > > >> label/rh.aparc.a2005s.annot mri/aparc+aseg > > >> .mgz > > >> check to see if all files exist... > > >> AD_C165 missing output files > > >> AD_C165 has no surf/lh.rh.sphere.reg > > >> > > >> In recon_all_status_log_checker > > >> > > >> > > WARNING: > /working/pthiyyagura/freesurfer/data_checker/data_checker/sample-recon-all-status.log > > >> does not exist. Skipping this > > >> complete status log file... > > >> > > >> ############# > > >> > > >> > > >> Its looking for lh.rh.sphere.reg. which would not exist. > > >> Could you please look into this. > > >> > > >> Thanks, > > >> Pradeep > > >> > > >> P.S also please chage > > >> set scriptsDir = > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> On Thu, Sep 16, 2010 at 11:41 AM, Nick Schmansky > > >> <ni...@nmr.mgh.harvard.edu > <mailto:ni...@nmr.mgh.harvard.edu>> wrote: > > >> > see also this page: > > >> > > > >> > http://surfer.nmr.mgh.harvard.edu/fswiki/QATools > > >> > > > >> > On Thu, 2010-09-16 at 14:13 -0400, Bruce Fischl wrote: > > >> >> Hi Avram, > > >> >> > > >> >> that all souds reasonable to me. > > >> >> > > >> >> cheers > > >> >> Bruce > > >> >> On Thu, 16 Sep 2010, Avram Holmes wrote: > > >> >> > > >> >> > All, > > >> >> > > > >> >> > I'm setting up a processing stream for a sizable > > dataset and I'd like > > >> >> > to use .tcl scripts to save out images for some > > preliminary quality > > >> >> > control checks. It was my intention to output images > > of the the > > >> >> > curvature and structural parcelation overlaid on the > > inflated surface > > >> >> > (6 views for each hemi) and the lh/rh.white and > > aseg.mgz segmentation > > >> >> > overlaid on the volume (a midline coronal, sagital, > > and axial slice). > > >> >> > The idea would be that then we could go through and > > quickly check > > >> >> > which subjects may need manual intervention. > > >> >> > > > >> >> > I wanted to double check that the images I am saving > > out are > > >> >> > consistent with the checks that other folks are doing > > and I'd love to > > >> >> > get some feedback on what else I should look save. > > >> >> > > > >> >> > Thanks, > > >> >> > Avram > > >> >> > > > >> >> > > > >> >> _______________________________________________ > > >> >> Freesurfer mailing list > > >> >> Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > >> >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> >> > > >> >> > > >> > > > >> > _______________________________________________ > > >> > Freesurfer mailing list > > >> > 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. > > >> > > > >> > > > >> > > >> > > >> > > > > > > > > > > > > > > > > > > -- > > Pradeep Thiyyagura > > Research Assistant > > School of Mathematical and Statistical Sciences > > Graduate Student > > Computational Biosciences > > Arizona State University > > Tempe, AZ 85287-1804 > > pradeep.thiyyag...@asu.edu <mailto:pradeep.thiyyag...@asu.edu> > > > > > > > > > > -- > > Pradeep Thiyyagura > > Research Assistant > > School of Mathematical and Statistical Sciences > > Graduate Student > > Computational Biosciences > > Arizona State University > > Tempe, AZ 85287-1804 > > pradeep.thiyyag...@asu.edu <mailto:pradeep.thiyyag...@asu.edu> > > > > ------------------------------ > > Message: 4 > Date: Sun, 19 Sep 2010 22:45:30 -0700 (PDT) > From: Siti Hajar <s.hajar...@yahoo.com <mailto:s.hajar...@yahoo.com>> > Subject: [Freesurfer] lh.thickness.fsaverage > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: <510347.11762...@web111606.mail.gq1.yahoo.com > <mailto:510347.11762...@web111606.mail.gq1.yahoo.com>> > Content-Type: text/plain; charset="us-ascii" > > When I run recon all for my subject, I couldn't open > lh.thickness.fsaverage.mgh > (/usr/local/freesurfer/subjects/.../surf/lh.thickness.fsaverage.mgh.) > I need to > use that information to obtain the cortical thickness.Is it because > the new > updated freesurfer or it might come from other source of problem? > > Thank you... > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20100919/52ae9974/attachment-0001.html > > > > ------------------------------ > > Message: 5 > Date: Mon, 20 Sep 2010 08:49:12 -0400 > From: Douglas Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] lh.thickness.fsaverage > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: <4c975848.3050...@nmr.mgh.harvard.edu > <mailto:4c975848.3050...@nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Siti, you'll need to give us more information about what you did. > What was your command line? Did the command finish without error? Have > you gone through the checks to make sure that the other results (eg, > skull strip) are ok? See > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > for what else might be useful to send to us so that we can more > efficiently help you. > > doug > > On 9/20/10 1:45 AM, Siti Hajar wrote: > > When I run recon all for my subject, I couldn't open > > lh.thickness.fsaverage.mgh > > (/usr/local/freesurfer/subjects/.../surf/lh.thickness.fsaverage.mgh.) > > I need to use that information to obtain the cortical thickness.Is it > > because the new updated freesurfer or it might come from other source > > of problem? > > > > Thank you... > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20100920/0c687aef/attachment.html > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 79, Issue 32 > ****************************************** > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
