Probably so On 10/10/2018 03:41 AM, Caroline Beelen wrote: > External Email - Use Caution > > Few clusters survive glm fit. No clusters seem to survive glm-fit-sim (when > visualizing). However, I'm not sure if I should also see this in a text file. > Opening cache.th40(or 30).abs.sig.cluster.summary it seems to have found no > clusters. At least, under the line ClusterNo Max VtxMax Size MNIX MNIY etc. > nothing is written. > > But does a lack of significant clusters also explain the weird messages of > "colortable with 1 entries read (originally none)" (& "CTABisEntryValid: > index -1 was OOB" & "Resource temporarily unavailable") that show up in the > terminal? > > Thanks very much, Caroline > > > > -----Oorspronkelijk bericht----- > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens > freesurfer-requ...@nmr.mgh.harvard.edu > Verzonden: dinsdag 9 oktober 2018 18:00 > Aan: freesurfer@nmr.mgh.harvard.edu > Onderwerp: Freesurfer Digest, Vol 176, Issue 9 > > Send Freesurfer mailing list submissions to > 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 > > You can reach the person managing the list at > 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. FW: RE: error glm-fit-sim (Caroline Beelen) > 2. Re: output values of vertices on surface into a textfile > (Sims, Sara A) > 3. Re: output values of vertices on surface into a textfile > (Bruce Fischl) > 4. Re: output values of vertices on surface into a textfile > (Sims, Sara A) > 5. Re: Hippocampal segmentation with an additional scan ERROR > kvlGEMSMatlab (Pradeep) > 6. Re: Hippocampal segmentation with an additional scan ERROR > kvlGEMSMatlab (Iglesias Gonzalez, Eugenio) > 7. hippocampal subfields (Marcel Heers) > 8. Re: hippocampal subfields (Iglesias Gonzalez, Eugenio) > 9. Re: Difference between 6.0.1 and 6.0.0 (Dicamillo, Robert) > 10. Talairach failed in monkey brain (Frehiwot Woldeyes) > 11. Re: FW: RE: error glm-fit-sim (Greve, Douglas N.,Ph.D.) > 12. Mri Convert Help (Justin Arnett) > 13. Re: Mri Convert Help (Greve, Douglas N.,Ph.D.) > 14. Re: Recon-all with/without T2 give the same stats > (Greve, Douglas N.,Ph.D.) > 15. Re: Recon-all with/without T2 give the same stats (Jianzhong Chen) > 16. m.khalil...@sutech.ac.ir sent you files via WeTransfer > (WeTransfer) > 17. very bad result using "mris_ca_train" and "mris_ca_label" > (Maedeh Khalilian) > 18. Re: Talairach failed in monkey brain (Greve, Douglas N.,Ph.D.) > 19. Re: Recon-all with/without T2 give the same stats > (Greve, Douglas N.,Ph.D.) > 20. Re: very bad result using "mris_ca_train" and "mris_ca_label" > (Bruce Fischl) > 21. Re: Extract individual vertex thickness values from cortical > parcellations (Greve, Douglas N.,Ph.D.) > 22. Re: nu_correct disk i/o issues (Greve, Douglas N.,Ph.D.) > 23. Re: masking cortical thickness (Greve, Douglas N.,Ph.D.) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 8 Oct 2018 16:12:06 +0000 > From: Caroline Beelen <caroline.bee...@kuleuven.be> > Subject: [Freesurfer] FW: RE: error glm-fit-sim > To: "freesurfer-boun...@nmr.mgh.harvard.edu" > <freesurfer-boun...@nmr.mgh.harvard.edu>, > "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <4051d561c94b40e0b641202b7bad7...@icts-s-exmbx25.luna.kuleuven.be> > Content-Type: text/plain; charset="us-ascii" > > External Email - Use Caution > > The command: > > gop@gop-linux:~/freesurfer$ freeview -f > $SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot > -viewport 3d > > The output: > > reading colortable from annotation file... > colortable with 1 entries read (originally none) > colortable with 1 entries read (originally none) > CTABisEntryValid: index -1 was OOB > Resource temporarily unavailable > Resource temporarily unavailable > B > ginally none) > CTABisEntryValid: index -1 was OOB > Resource temporarily unavailable > Resource temporarily unavailable > B > ginally none) > CTABisEntryValid: index -1 was OOB > Resource temporarily unavailable > Resource temporarily unavailable > B > ginally none) > > The command with a bit less strict significance level: > > gop@gop-linux:~/freesurfer$ freeview -f > $SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=3,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot > -viewport 3d > > The output: > > reading colortable from annotation file... > colortable with 1 entries read (originally none) > colortable with 1 entries read (originally none) > > (and then it says no more). > > Both commands visualize the data, but no clusters are found. > Is this how it should be? Does it mean that there is a problem with reading > colortables or not? > > Best, Caroline > > Message: 2 > Date: Mon, 1 Oct 2018 17:10:28 +0000 > From: "Greve, Douglas N.,Ph.D." > <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> > Subject: Re: [Freesurfer] error glm-fit-sim > To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: > <504d6069-399f-163d-39a9-dcc6c02d3...@mgh.harvard.edu<mailto:504d6069-399f-163d-39a9-dcc6c02d3...@mgh.harvard.edu>> > Content-Type: text/plain; charset="Windows-1252" > > What says that? What command are you running? What is the other terminal > output? > > > On 10/01/2018 04:54 AM, Caroline Beelen wrote: >> ????????External Email - Use Caution >> >> Dear FS, >> >> I followed the group analysis page for glm analysis and it worked fine >> until the final step. I?m using version 5.3. After performing >> glm-fit-sim it says ?glm-fit done? (for all files), but when trying to >> open these it says: >> >> ?Reading colortable from annotation file? >> >> Colortable with 1 entries read (originally none) >> >> Colortable with 1 entries read (originally none) >> >> CTABisentryvalid: index -1 was 00B >> >> Resource temporarily unavailable >> >> CTABisentryvalid: index -1 was 00B >> >> Resource temporarily unavailable >> >> Resource temporarily unavailable? >> >> (etc..) >> >> It opens, but nothing is visible and I have the feeling it cannot open >> color files?? >> >> MRI glmfit gives positive clusters for some values. I therefore used >> the abs sign for glm-fit-sim. >> >> What might be wrong? >> >> Thanks. Caroline > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20181008/146db99d/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Mon, 8 Oct 2018 16:22:05 +0000 > From: "Sims, Sara A" <sno...@uab.edu> > Subject: Re: [Freesurfer] output values of vertices on surface into a > textfile > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <ecdb6fbd-f8ff-4186-8e87-2b557bff8...@uab.edu> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Doug, > I'm sorry. It is actually a surface overlay. So same question but about > overlays: How could I output the location and value information? > > Sara Sims > > ?On 10/3/18, 12:10 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > Greve, Douglas N.,Ph.D." <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > dgr...@mgh.harvard.edu> wrote: > > mris_convert lh.white lh.white.asc will convert it to ascii. This file > will have both xyz coordinates and neighborhood relationships, so you'll > have to delete the latter. You can also load the surface into matlab > with read_surf.m > > On 10/03/2018 11:48 AM, Sims, Sara A wrote: > > > > External Email - Use Caution > > > > Hello! > > > > I would like to output the location and value of each vertex on a > > surface to a text file. How could I go about doing this? > > > > Thanks, > > > > Sara Sims > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ------------------------------ > > Message: 3 > Date: Mon, 8 Oct 2018 12:30:03 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] output values of vertices on surface into a > textfile > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.20.1810081229340.20...@gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Sara > > something like: > > > mris_convert -c lh.your_overlay lh.white lh.your_overlay.asc > > should do the trick > > cheers > Bruce > On Mon, 8 Oct > 2018, Sims, Sara A wrote: > >> External Email - Use Caution >> >> Doug, >> I'm sorry. It is actually a surface overlay. So same question but about >> overlays: How could I output the location and value information? >> >> Sara Sims >> >> ?On 10/3/18, 12:10 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of >> Greve, Douglas N.,Ph.D." <freesurfer-boun...@nmr.mgh.harvard.edu on behalf >> of dgr...@mgh.harvard.edu> wrote: >> >> mris_convert lh.white lh.white.asc will convert it to ascii. This file >> will have both xyz coordinates and neighborhood relationships, so you'll >> have to delete the latter. You can also load the surface into matlab >> with read_surf.m >> >> On 10/03/2018 11:48 AM, Sims, Sara A wrote: >> > >> > External Email - Use Caution >> > >> > Hello! >> > >> > I would like to output the location and value of each vertex on a >> > surface to a text file. How could I go about doing this? >> > >> > Thanks, >> > >> > Sara Sims >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ------------------------------ > > Message: 4 > Date: Mon, 8 Oct 2018 17:04:31 +0000 > From: "Sims, Sara A" <sno...@uab.edu> > Subject: Re: [Freesurfer] output values of vertices on surface into a > textfile > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <1c29e5fa-e23d-42e1-a4d6-56dcbf63e...@uab.edu> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Thanks so much! > > Sara Sims > Graduate Research Fellow > University of Alabama at Birmingham > Department of Psychology > 205-975-4060 > sno...@uab.edu > > ?On 10/8/18, 11:30 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > Bruce Fischl" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > fis...@nmr.mgh.harvard.edu> wrote: > > Hi Sara > > something like: > > > mris_convert -c lh.your_overlay lh.white lh.your_overlay.asc > > should do the trick > > cheers > Bruce > On Mon, 8 Oct > 2018, Sims, Sara A wrote: > > > External Email - Use Caution > > > > Doug, > > I'm sorry. It is actually a surface overlay. So same question but > about overlays: How could I output the location and value information? > > > > Sara Sims > > > > On 10/3/18, 12:10 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on > behalf of Greve, Douglas N.,Ph.D." <freesurfer-boun...@nmr.mgh.harvard.edu on > behalf of dgr...@mgh.harvard.edu> wrote: > > > > mris_convert lh.white lh.white.asc will convert it to ascii. This > file > > will have both xyz coordinates and neighborhood relationships, so > you'll > > have to delete the latter. You can also load the surface into matlab > > with read_surf.m > > > > On 10/03/2018 11:48 AM, Sims, Sara A wrote: > > > > > > External Email - Use Caution > > > > > > Hello! > > > > > > I would like to output the location and value of each vertex on a > > > surface to a text file. How could I go about doing this? > > > > > > Thanks, > > > > > > Sara Sims > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > ------------------------------ > > Message: 5 > Date: Mon, 8 Oct 2018 10:49:17 -0700 > From: Pradeep <tprad...@gmail.com> > Subject: Re: [Freesurfer] Hippocampal segmentation with an additional > scan ERROR kvlGEMSMatlab > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <capxm4xnawvpapmxfxephh_qcy_z04sdxa07hbxec+putpb4...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi Iglesias, > > It turns out that my input images are in different orientation and I had a > hard time reorienting them. > Starting from dicom images and using mri_convert to bring them to nifti > format seem to fix the problem > The hippocampal subfiled segmentation program with the additional high > resolution scan works! > > > Thank you for all the help! > > Pradeep > > On Thu, Oct 4, 2018 at 11:28 AM Iglesias Gonzalez, Eugenio < > e.igles...@ucl.ac.uk> wrote: > >> External Email - Use Caution >> >> Thanks! >> >> Did you check whether the T2 and the T1 were correctly registered? You can >> check out the animated gif under mri/transforms in the subject?s directory. >> >> Cheers, >> >> /E >> >> >> >> -- >> >> Juan Eugenio Iglesias >> >> ERC Senior Research Fellow >> >> Centre for Medical Image Computing (CMIC) >> >> University College London >> >> http://www.jeiglesias.com >> >> http://cmictig.cs.ucl.ac.uk/ >> >> >> >> >> >> *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Pradeep < >> tprad...@gmail.com> >> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> *Date: *Thursday, 4 October 2018 at 19:21 >> *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> *Subject: *Re: [Freesurfer] Hippocampal segmentation with an additional >> scan ERROR kvlGEMSMatlab >> >> >> >> * External Email - Use Caution * >> >> I have tried this for two subjects and got the same error. >> >> >> >> Thanks, >> Pradeep >> >> >> >> On Thu, Oct 4, 2018 at 11:14 AM Iglesias Gonzalez, Eugenio < >> e.igles...@ucl.ac.uk> wrote: >> >> * External Email - Use Caution * >> >> Dear Pradeep, >> >> Did you get this error on several subjects, or only one? >> >> Cheers, >> >> /Eugenio >> >> >> >> -- >> >> Juan Eugenio Iglesias >> >> ERC Senior Research Fellow >> >> Centre for Medical Image Computing (CMIC) >> >> University College London >> >> http://www.jeiglesias.com >> >> http://cmictig.cs.ucl.ac.uk/ >> >> >> >> >> >> *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Pradeep < >> tprad...@gmail.com> >> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> *Date: *Thursday, 4 October 2018 at 19:12 >> *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> *Subject: *[Freesurfer] Hippocampal segmentation with an additional scan >> ERROR kvlGEMSMatlab >> >> >> >> * External Email - Use Caution * >> >> Hello, >> >> >> >> I am trying to run the hippocampal segmentation with an additional Hi-res >> scan using the following command >> >> recon-all -s <subject_name> -hippocampal-subfields-T2 <file name of >> additional scan> <analysisID> >> >> and got the following error >> >> >> >> >> >> Error using kvlGEMSMatlab >> >> >> /autofs/cluster/koen/eugenio/InsightToolkit-4.9.1/Modules/Core/Common/include/itkImageConstIterator.h:211: >> >> itk::ERROR: Region ImageRegion (0x7f67011c5dd0) >> >> Dimension: 3 >> >> Index: [0, 845, 0] >> >> Size: [105, 18446744073709550952, 20] >> >> is outside of buffered region ImageRegion (0x7f6573ca8bb8) >> >> Dimension: 3 >> >> Index: [0, 0, 0] >> >> Size: [526, 181, 526] >> >> >> >> Error in kvlReadCroppedImage (line 11) >> >> Error in segmentSubjectT2_autoEstimateAlveusML (line 838) >> >> Started at Thu Oct 4 09:35:38 MST 2018 >> >> Ended at Thu Oct 4 09:57:35 MST 2018 >> >> #@#%# recon-all-run-time-hours 0.366 >> >> recon-all -s subject_id finished without error at Thu Oct 4 09:57:36 MST >> 2018 >> >> done >> >> >> >> >> >> I came across a similar error in the forums and using the most recent >> version seem to have worked for some, but it did not help in my case. >> >> >> >> Freesurfer version I am using >> >> Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a >> >> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a >> >> >> >> with matlab run time from 2012b as suggested >> >> I have also tried to use 2014b runtime which exited right away. >> >> >> >> Thank you for your help, >> >> Pradeep >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> 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/20181008/1046833d/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Mon, 8 Oct 2018 17:52:30 +0000 > From: "Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk> > Subject: Re: [Freesurfer] Hippocampal segmentation with an additional > scan ERROR kvlGEMSMatlab > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <6d8c46d2-662a-4228-b26b-c99e349e1...@ucl.ac.uk> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Glad to hear. > As much as it exists to solve problems, it?s also nice to get positive news > on the list every once in a while. > Cheers, > /E > > -- > Juan Eugenio Iglesias > ERC Senior Research Fellow > Centre for Medical Image Computing (CMIC) > University College London > http://www.jeiglesias.com > http://cmictig.cs.ucl.ac.uk/ > > > From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Pradeep > <tprad...@gmail.com> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Date: Monday, 8 October 2018 at 18:51 > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Hippocampal segmentation with an additional scan > ERROR kvlGEMSMatlab > > > External Email - Use Caution > Hi Iglesias, > > It turns out that my input images are in different orientation and I had a > hard time reorienting them. > Starting from dicom images and using mri_convert to bring them to nifti > format seem to fix the problem > The hippocampal subfiled segmentation program with the additional high > resolution scan works! > > > Thank you for all the help! > > Pradeep > > On Thu, Oct 4, 2018 at 11:28 AM Iglesias Gonzalez, Eugenio > <e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>> wrote: > > External Email - Use Caution > Thanks! > Did you check whether the T2 and the T1 were correctly registered? You can > check out the animated gif under mri/transforms in the subject?s directory. > Cheers, > /E > > -- > Juan Eugenio Iglesias > ERC Senior Research Fellow > Centre for Medical Image Computing (CMIC) > University College London > http://www.jeiglesias.com > http://cmictig.cs.ucl.ac.uk/ > > > From: > <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> > on behalf of Pradeep <tprad...@gmail.com<mailto:tprad...@gmail.com>> > Reply-To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Thursday, 4 October 2018 at 19:21 > To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] Hippocampal segmentation with an additional scan > ERROR kvlGEMSMatlab > > > External Email - Use Caution > I have tried this for two subjects and got the same error. > > Thanks, > Pradeep > > On Thu, Oct 4, 2018 at 11:14 AM Iglesias Gonzalez, Eugenio > <e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>> wrote: > > External Email - Use Caution > Dear Pradeep, > Did you get this error on several subjects, or only one? > Cheers, > /Eugenio > > -- > Juan Eugenio Iglesias > ERC Senior Research Fellow > Centre for Medical Image Computing (CMIC) > University College London > http://www.jeiglesias.com > http://cmictig.cs.ucl.ac.uk/ > > > From: > <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> > on behalf of Pradeep <tprad...@gmail.com<mailto:tprad...@gmail.com>> > Reply-To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Thursday, 4 October 2018 at 19:12 > To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: [Freesurfer] Hippocampal segmentation with an additional scan ERROR > kvlGEMSMatlab > > > External Email - Use Caution > Hello, > > I am trying to run the hippocampal segmentation with an additional Hi-res > scan using the following command > > recon-all -s <subject_name> -hippocampal-subfields-T2 <file name of > additional scan> <analysisID> > and got the following error > > > Error using kvlGEMSMatlab > /autofs/cluster/koen/eugenio/InsightToolkit-4.9.1/Modules/Core/Common/include/itkImageConstIterator.h:211: > itk::ERROR: Region ImageRegion (0x7f67011c5dd0) > Dimension: 3 > Index: [0, 845, 0] > Size: [105, 18446744073709550952, 20] > is outside of buffered region ImageRegion (0x7f6573ca8bb8) > Dimension: 3 > Index: [0, 0, 0] > Size: [526, 181, 526] > > Error in kvlReadCroppedImage (line 11) > Error in segmentSubjectT2_autoEstimateAlveusML (line 838) > Started at Thu Oct 4 09:35:38 MST 2018 > Ended at Thu Oct 4 09:57:35 MST 2018 > #@#%# recon-all-run-time-hours 0.366 > recon-all -s subject_id finished without error at Thu Oct 4 09:57:36 MST 2018 > done > > > I came across a similar error in the forums and using the most recent version > seem to have worked for some, but it did not help in my case. > > Freesurfer version I am using > Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a > Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a > > with matlab run time from 2012b as suggested > I have also tried to use 2014b runtime which exited right away. > > Thank you for your help, > Pradeep > > > > > > _______________________________________________ > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20181008/6b5820c2/attachment-0001.html > > ------------------------------ > > Message: 7 > Date: Mon, 8 Oct 2018 21:44:41 +0200 > From: Marcel Heers <marcel.he...@gmail.com> > Subject: [Freesurfer] hippocampal subfields > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <CAMq9WnPVgt=JvowRyD_QO=t_qbruf3ncjl-6aiogf4itxw6...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Dear Eugenio, > > there is one error in the error.log: 'Could not set locale'. > > Best regards > > Marcel > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20181008/95ffe948/attachment-0001.html > > ------------------------------ > > Message: 8 > Date: Mon, 8 Oct 2018 19:47:18 +0000 > From: "Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk> > Subject: Re: [Freesurfer] hippocampal subfields > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <ef84e1ec-2bae-4717-8278-ff2fadf51...@ucl.ac.uk> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Thanks, Marcel. Can you please send us the whole output (can be found in the > log file) > Cheers, > /E > > -- > Juan Eugenio Iglesias > ERC Senior Research Fellow > Centre for Medical Image Computing (CMIC) > University College London > http://www.jeiglesias.com > http://cmictig.cs.ucl.ac.uk/ > > > From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Marcel Heers > <marcel.he...@gmail.com> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Date: Monday, 8 October 2018 at 20:45 > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Subject: [Freesurfer] hippocampal subfields > > > External Email - Use Caution > Dear Eugenio, > > there is one error in the error.log: 'Could not set locale'. > > Best regards > > Marcel > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20181008/f521c562/attachment-0001.html > > ------------------------------ > > Message: 9 > Date: Mon, 8 Oct 2018 20:26:53 +0000 > From: "Dicamillo, Robert" <rdicami...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Difference between 6.0.1 and 6.0.0 > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <f388d7af-ea87-43ac-998e-21992fff3...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hello Haakon, > > I don?t there are significant functionality changes in the 6.0.1 patch > release. i think there are however changes to fix some run time errors with > respect to system libraries found/used on the system running Freesurfer. > Someone else who mentors the help list might chime in, but I don?t know of a > reason to use 6.0.0 instead of the 6.0.1 release. > > - rob > > On Oct 8, 2018, at 9:46 AM, Haakon Ramsland Hol > <haakon.ramsland....@sshf.no<mailto:haakon.ramsland....@sshf.no>> wrote: > > > External Email - Use Caution > > Dear Experts. > > I just happened to stumble across version 6.0.1, what is the main difference > from 6.0.0? And I read in a post from 2017 that the flairpial wasn?t > optimized in v6.0.0 compared to 5.3, and that this would be optimized in > version 6.1. Any news with regards to flair pial? Is it recommended to use > 5.3 if you have flair images as well? > > Kind regards. > > Haakon R. Hol > Radiologist. > _______________________________________________ > 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/20181008/5673f422/attachment-0001.html > > ------------------------------ > > Message: 10 > Date: Mon, 8 Oct 2018 16:28:06 -0500 > From: Frehiwot Woldeyes <fwol...@uic.edu> > Subject: [Freesurfer] Talairach failed in monkey brain > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <CAOcOQ6X3xp-5VkczfqNzq2LPh8f4xRTEDQCnsJFknDrJ=dq...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hello Freesurfers, > > I was attempting to reconstruct a monkey brain, i encountered an error > during talairach registration step, i have used tkregister2 to manually > edit the registration but i have gotten error there too: > > tkregister2 --targ > /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii --mov > /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii --reg > /usr/local/freesurfer/subjects/A004_crop.mhd.nii > tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl > target volume > /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii > movable volume > /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii > reg file /usr/local/freesurfer/subjects/A004_crop.mhd.nii > LoadVol 1 > ZeroCRAS 0 > $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ > Diagnostic Level -1 > regio_read_register(): No such file or directory > Could not open /usr/local/freesurfer/subjects/A004_crop.mhd.nii > ERROR: reading /usr/local/freesurfer/subjects/A004_crop.mhd.nii > > Do you have any thoughts on how to troubleshoot this one? > > Regards, > frehiwot > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20181008/1e20902b/attachment-0001.html > > ------------------------------ > > Message: 11 > Date: Tue, 9 Oct 2018 01:36:00 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] FW: RE: error glm-fit-sim > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <de22c9d7-6339-de75-8147-a98669c16...@mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > were there any clusters that survived? > > On 10/8/18 12:12 PM, Caroline Beelen wrote: > > External Email - Use Caution > The command: > > gop@gop-linux:~/freesurfer$ freeview -f > $SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot > -viewport 3d > > The output: > > reading colortable from annotation file... > colortable with 1 entries read (originally none) > colortable with 1 entries read (originally none) > CTABisEntryValid: index -1 was OOB > Resource temporarily unavailable > Resource temporarily unavailable > B > ginally none) > CTABisEntryValid: index -1 was OOB > Resource temporarily unavailable > Resource temporarily unavailable > B > ginally none) > CTABisEntryValid: index -1 was OOB > Resource temporarily unavailable > Resource temporarily unavailable > B > ginally none) > > The command with a bit less strict significance level: > > gop@gop-linux:~/freesurfer$ freeview -f > $SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=3,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot > -viewport 3d > > The output: > > reading colortable from annotation file... > colortable with 1 entries read (originally none) > colortable with 1 entries read (originally none) > > (and then it says no more). > > Both commands visualize the data, but no clusters are found. > Is this how it should be? Does it mean that there is a problem with reading > colortables or not? > > Best, Caroline > > Message: 2 > Date: Mon, 1 Oct 2018 17:10:28 +0000 > From: "Greve, Douglas N.,Ph.D." > <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> > Subject: Re: [Freesurfer] error glm-fit-sim > To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: > <504d6069-399f-163d-39a9-dcc6c02d3...@mgh.harvard.edu<mailto:504d6069-399f-163d-39a9-dcc6c02d3...@mgh.harvard.edu>> > Content-Type: text/plain; charset="Windows-1252" > > What says that? What command are you running? What is the other terminal > output? > > > On 10/01/2018 04:54 AM, Caroline Beelen wrote: >> ????????External Email - Use Caution >> >> Dear FS, >> >> I followed the group analysis page for glm analysis and it worked fine >> until the final step. I?m using version 5.3. After performing >> glm-fit-sim it says ?glm-fit done? (for all files), but when trying to >> open these it says: >> >> ?Reading colortable from annotation file? >> >> Colortable with 1 entries read (originally none) >> >> Colortable with 1 entries read (originally none) >> >> CTABisentryvalid: index -1 was 00B >> >> Resource temporarily unavailable >> >> CTABisentryvalid: index -1 was 00B >> >> Resource temporarily unavailable >> >> Resource temporarily unavailable? >> >> (etc..) >> >> It opens, but nothing is visible and I have the feeling it cannot open >> color files?? >> >> MRI glmfit gives positive clusters for some values. I therefore used >> the abs sign for glm-fit-sim. >> >> What might be wrong? >> >> Thanks. Caroline > > > > _______________________________________________ > 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/20181009/b7dab327/attachment-0001.html > > ------------------------------ > > Message: 12 > Date: Mon, 8 Oct 2018 21:54:03 -0400 > From: Justin Arnett <jnett...@gmail.com> > Subject: [Freesurfer] Mri Convert Help > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <canjdyqk7yk4mfmdnkthyvv1u4cy8vsiczz_ssjzcvfd7hmi...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hello Everyone, > I hope you are doing well! > > I am trying to recon-all a DICOM file, for the ultimate hope of being able > to identify the location of M1 via parcellation. I have successfully been > able to do so for 2 subjects already, though for some reason I am having a > problem with the MRI convert stage from the .dcm file to the .nii.gz file. > I copied/pasted the terminal shell I tried performing above. I am using a > Mac (Yosemite 10.10.5) with FreeSurfer V6.0.0 > > Further, I think it might be helpful to note that I am a very extreme > novice in computer science/coding--I have completed recon-all's of 2 > subjects by following, essentially line-by-line, the "FreeSurfer Download > and Install Page," and this process was the first time I ever used the > terminal shell. (In this way, I would absolutely LOVE if anyone might be > able to explain where I went wrong as simplistically as possible). > > Thank you all so much for the help- I hope you have a great start to the > week! > - Justin > > > DBI 05 MRI Convert Error > > > > > > Justins-Computer:~ justinarnett$ export > FREESURFER_HOME=/Applications/freesurfer > > Justins-Computer:~ justinarnett$ source $FREESURFER_HOME/SetUpFreeSurfer.sh > > -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME /Applications/freesurfer > > FSFAST_HOME /Applications/freesurfer/fsfast > > FSF_OUTPUT_FORMAT nii.gz > > SUBJECTS_DIR /Applications/freesurfer/subjects > > -bash: [: /Users/justinarnett: binary operator expected > > grep: /Users/justinarnett: Is a directory > > grep: 1/matlab/startup.m: No such file or directory > > grep: /Users/justinarnett: Is a directory > > grep: 1/matlab/startup.m: No such file or directory > > grep: /Users/justinarnett: Is a directory > > grep: 1/matlab/startup.m: No such file or directory > > MNI_DIR /Applications/freesurfer/mni > > Justins-Computer:~ justinarnett$ export > SUBJECTS_DIR=/Applications/freesurfer/subjects/DBI05MRI > > Justins-Computer:~ justinarnett$ cd > /Applications/freesurfer/subjects/DBI05MRI > > Justins-Computer:DBI05MRI justinarnett$ cp > $FREESURFER_HOME/subjects/DBI05MRI/Image1.dcm > > usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file > > cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... > target_directory > > Justins-Computer:DBI05MRI justinarnett$ mri_convert Image1.dcm Image1.nii.gz > > /Applications/freesurfer/FreeSurferEnv.sh: line 226: [: > /Users/justinarnett: binary operator expected > > grep: /Users/justinarnett: Is a directory > > grep: 1/matlab/startup.m: No such file or directory > > grep: /Users/justinarnett: Is a directory > > grep: 1/matlab/startup.m: No such file or directory > > grep: /Users/justinarnett: Is a directory > > grep: 1/matlab/startup.m: No such file or directory > > mri_convert.bin Image1.dcm Image1.nii.gz > > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > > reading from Image1.dcm... > > Starting DICOMRead2() > > dcmfile = /Applications/freesurfer/subjects/DBI05MRI/Image1.dcm > > dcmdir = /Applications/freesurfer/subjects/DBI05MRI > > Ref Series No = 401 > > Found 824 files, checking for dicoms > > WARNING: tag ImageNumber not found in > /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR > > WARNING: tag SeriesNumber not found in > /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR > > WARNING: tag image orientation not found in > /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR > > ERROR: GetDICOMInfo(): dcmGetDWIParams() 10 > > DICOM File: /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR > > break DICOMRead.c:5228 > > Found 164 dicom files in series. > > WARNING: tag ImageNumber not found in > /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR > > WARNING: tag SeriesNumber not found in > /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR > > WARNING: tag image orientation not found in > /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR > > ERROR: GetDICOMInfo(): dcmGetDWIParams() 10 > > DICOM File: /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR > > break DICOMRead.c:5228 > > First Sorting > > Computing Slice Direction > > Vs: -120.054 -103.192 34.4639 > > Vs: -0.741 -0.636922 0.212719 > > Second Sorting > > IsDWI = 0, IsPhilipsDWI = 0 > > Counting frames > > nframes = 1 > > nslices = 165 > > ndcmfiles = 165 > > MRIallocSequence(0, 0, 165, 1): bad parm > > No such file or directory > > ERROR: mri alloc failed > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20181008/8c8b227f/attachment-0001.html > > ------------------------------ > > Message: 13 > Date: Tue, 9 Oct 2018 02:13:41 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Mri Convert Help > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <01adef19-678e-6a11-1de4-9a1f5838a...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Sorry, there are a lot of things going on down there, it is hard to figure > out what is happening. It looks like the sourcing of SetUpFreeSurfer.sh is > failing is that right? Then it looks like the copy (cp) is failing. Then when > you run mri_convert, it looks like another bash error. It looks like > mri_convert is trying to unpack it as a diffusion file and that may be what > is causing the final error. Try > export FS_LOAD_DWI=0 > > > On 10/8/18 9:54 PM, Justin Arnett wrote: > > > > Hello Everyone, > I hope you are doing well! > > I am trying to recon-all a DICOM file, for the ultimate hope of being able to > identify the location of M1 via parcellation. I have successfully been able > to do so for 2 subjects already, though for some reason I am having a problem > with the MRI convert stage from the .dcm file to the .nii.gz file. I > copied/pasted the terminal shell I tried performing above. I am using a Mac > (Yosemite 10.10.5) with FreeSurfer V6.0.0 > > Further, I think it might be helpful to note that I am a very extreme novice > in computer science/coding--I have completed recon-all's of 2 subjects by > following, essentially line-by-line, the "FreeSurfer Download and Install > Page," and this process was the first time I ever used the terminal shell. > (In this way, I would absolutely LOVE if anyone might be able to explain > where I went wrong as simplistically as possible). > > Thank you all so much for the help- I hope you have a great start to the week! > - Justin > > > DBI 05 MRI Convert Error > > > Justins-Computer:~ justinarnett$ export > FREESURFER_HOME=/Applications/freesurfer > Justins-Computer:~ justinarnett$ source $FREESURFER_HOME/SetUpFreeSurfer.sh > -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /Applications/freesurfer > FSFAST_HOME /Applications/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /Applications/freesurfer/subjects > -bash: [: /Users/justinarnett: binary operator expected > grep: /Users/justinarnett: Is a directory > grep: 1/matlab/startup.m: No such file or directory > grep: /Users/justinarnett: Is a directory > grep: 1/matlab/startup.m: No such file or directory > grep: /Users/justinarnett: Is a directory > grep: 1/matlab/startup.m: No such file or directory > MNI_DIR /Applications/freesurfer/mni > Justins-Computer:~ justinarnett$ export > SUBJECTS_DIR=/Applications/freesurfer/subjects/DBI05MRI > Justins-Computer:~ justinarnett$ cd /Applications/freesurfer/subjects/DBI05MRI > Justins-Computer:DBI05MRI justinarnett$ cp > $FREESURFER_HOME/subjects/DBI05MRI/Image1.dcm > usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file > cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... > target_directory > Justins-Computer:DBI05MRI justinarnett$ mri_convert Image1.dcm Image1.nii.gz > /Applications/freesurfer/FreeSurferEnv.sh: line 226: [: /Users/justinarnett: > binary operator expected > grep: /Users/justinarnett: Is a directory > grep: 1/matlab/startup.m: No such file or directory > grep: /Users/justinarnett: Is a directory > grep: 1/matlab/startup.m: No such file or directory > grep: /Users/justinarnett: Is a directory > grep: 1/matlab/startup.m: No such file or directory > mri_convert.bin Image1.dcm Image1.nii.gz > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > reading from Image1.dcm... > Starting DICOMRead2() > dcmfile = /Applications/freesurfer/subjects/DBI05MRI/Image1.dcm > dcmdir = /Applications/freesurfer/subjects/DBI05MRI > Ref Series No = 401 > Found 824 files, checking for dicoms > WARNING: tag ImageNumber not found in > /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR > WARNING: tag SeriesNumber not found in > /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR > WARNING: tag image orientation not found in > /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR > ERROR: GetDICOMInfo(): dcmGetDWIParams() 10 > DICOM File: /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR > break DICOMRead.c:5228 > Found 164 dicom files in series. > WARNING: tag ImageNumber not found in > /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR > WARNING: tag SeriesNumber not found in > /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR > WARNING: tag image orientation not found in > /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR > ERROR: GetDICOMInfo(): dcmGetDWIParams() 10 > DICOM File: /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR > break DICOMRead.c:5228 > First Sorting > Computing Slice Direction > Vs: -120.054 -103.192 34.4639 > Vs: -0.741 -0.636922 0.212719 > Second Sorting > IsDWI = 0, IsPhilipsDWI = 0 > Counting frames > nframes = 1 > nslices = 165 > ndcmfiles = 165 > MRIallocSequence(0, 0, 165, 1): bad parm > No such file or directory > ERROR: mri alloc failed > > > > _______________________________________________ > 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/20181009/2ff05c9d/attachment-0001.html > > ------------------------------ > > Message: 14 > Date: Tue, 9 Oct 2018 02:16:03 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Recon-all with/without T2 give the same > stats > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <5a4dbcee-d903-f4b9-a946-05a9e51cc...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > The aseg.stats should be the same since that does not make reference to the > surfaces. The aparc stats should have been different because the thickness > should have been different. Can you check whether the thickness files are > different? > > On 10/8/18 9:39 AM, Jianzhong Chen wrote: > > External Email - Use Caution > > Dear All, > > I tried recon-all with/without T2 image using FS 5.3.0. Then I found that the > aseg stats and aparc stats with/without T2 are exactly the same. When I check > the pial surfaces, I can see that they are very similar but not the same. So > is it reasonable to see exactly the same stats? > An example of the pial surfaces with/without T2 is attached here. The red > line is lh.pial with T2 and the yellow line is the lh.pial without T2 > My command for recon-all with T2 is: recon-all -s ${subject} -i T1.nii -all > -T2 T2.nii -T2pial -sd ${T2_dir} > My command for recon-all without T2 is: recon-all -s ${subject} -i T1.nii > -all -sd ${T1_dir} > > Thanks, > Jianzhong > > > > _______________________________________________ > 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/20181009/dc25e9c5/attachment-0001.html > > ------------------------------ > > Message: 15 > Date: Tue, 9 Oct 2018 13:46:03 +0800 > From: Jianzhong Chen <chenjianzhong1...@gmail.com> > Subject: Re: [Freesurfer] Recon-all with/without T2 give the same > stats > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <CAAVOdwbXCgCJqX_BmwbSPX4+uHT8R2N9esr=b9=hd-+xxne...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi Dr. Greve, > > I checked the lh.aparc.stats and rh.aparc.stats, the thicknesses (and the > other measures like volume and area) are all the same. > > Thanks, > Jianzhong > > Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> ?2018?10?9??? ??10:16??? > >> The aseg.stats should be the same since that does not make reference to >> the surfaces. The aparc stats should have been different because the >> thickness should have been different. Can you check whether the thickness >> files are different? >> >> On 10/8/18 9:39 AM, Jianzhong Chen wrote: >> >> External Email - Use Caution >> Dear All, >> >> I tried recon-all with/without T2 image using FS 5.3.0. Then I found that >> the aseg stats and aparc stats with/without T2 are exactly the same. When I >> check the pial surfaces, I can see that they are very similar but not the >> same. So is it reasonable to see exactly the same stats? >> An example of the pial surfaces with/without T2 is attached here. The red >> line is lh.pial with T2 and the yellow line is the lh.pial without T2 >> My command for recon-all with T2 is: recon-all -s ${subject} -i T1.nii >> -all -T2 T2.nii -T2pial -sd ${T2_dir} >> My command for recon-all without T2 is: recon-all -s ${subject} -i T1.nii >> -all -sd ${T1_dir} >> >> Thanks, >> Jianzhong >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> 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/20181009/f483cf13/attachment-0001.html > > ------------------------------ > > Message: 16 > Date: Tue, 09 Oct 2018 11:47:05 +0000 (UTC) > From: WeTransfer <nore...@wetransfer.com> > Subject: [Freesurfer] m.khalil...@sutech.ac.ir sent you files via > WeTransfer > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <wtm.34a5f7f8-79fc-432e-83f4-6a060ae67...@wetransfer.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > m.khalil...@sutech.ac.ir sent you some files > > 1 file, 378 MB in total > ? Will be deleted on 16 October, 2018 > > > Download link: > https://wetransfer.com/downloads/9370a847d04b46d6fcbc4faec24f094e20181009110257/83dcd2124cf5da491c194f833e0c804c20181009110257/327c62 > > > Message: > Dear Dr.Bruce Fischl > Thank you very much for your great sense of responsibility. > Sure, i have attached a zip file named "Maedeh_results"(it was a rather big > sized one so i > had to send it through Wetranser). It contains my initial annotation files(as > the input of > 'mris_ca-train') by which i have made my atlas(?h.Desikan100.annot), my > atlases for both > hemispheres(?hDesikan100.gcs), a color LUT, my subject directory "test1" > which i have used > as the input of "mris_ca_train", another subject diectory "subj1", on which i > have used to > test my atlas, and finally my results "?h.finalDesikan100.annot" .(actually > the result of > applying my atlas on subj1) > i myself guess that the main problem is that i am using just one subject as > the input of > "mris_ca_train", but i dunno how to get multiple subjects... > that would be perfect if you could help me. > Cheers > Maedeh. > > > > 1 file > > Maedeh_results.zip > > > [Get more out of WeTransfer, get > Plus](https://wetransfer.com/plus?trk=WT201704_email&utm_campaign=WT_email_tracking&utm_content=general&utm_medium=plus_footer_ad_link&utm_source=notify_recipient_email) > > > > About WeTransfer: https://wetransfer.com/about > Help: https://wetransfer.zendesk.com/hc/en-us > Legal: https://wetransfer.com/legal/terms > > > To make sure our emails arrive, please add nore...@wetransfer.com to [your > contacts](https://wetransfer.zendesk.com/hc/en-us/articles/204909429). > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20181009/d45bfacd/attachment-0001.html > > ------------------------------ > > Message: 17 > Date: Tue, 09 Oct 2018 15:50:34 +0330 > From: "Maedeh Khalilian" <m.khalil...@sutech.ac.ir> > Subject: [Freesurfer] very bad result using "mris_ca_train" and > "mris_ca_label" > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <wc20181009122034.210...@sutech.ac.ir> > Content-Type: text/plain; charset="us-ascii" > > External Email - Use Caution > > Dear Dr.Bruce Fischl > Thank you very much for your great sense of responsibility. > Sure, i have sent you a zip file named "Maedeh_results"(it was a rather big > sized one so i had to send it through Wetranser). Hope you have received it. > However, a general question is that, according to freesurfer help the > required arguments for "mris_ca_train" are : > mris_ca_train [options] <hemi> <canon surf> <annot file> <subject 1> > <subject 2> ... <output file> > > as it seems it gets one surf file(e.g sphere.reg),and one annotation file, > but several subjects...so what does this surface file refer to?should i make > an average of all subjects' .reg files? and also for the annotation file ! > just one .annot is enough or i have to make an average of several annotation > files? > if yes, how should i do that? > i would be grateful if you could help me. > Best regards > Maedeh, > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20181009/d2a951de/attachment-0001.html > > ------------------------------ > > Message: 18 > Date: Tue, 9 Oct 2018 14:17:52 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Talairach failed in monkey brain > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <e8ac8b29-d5ad-2fc5-ca41-d1049ae60...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > The file passed to --reg should be a registration file. This is a text file > with the transformation matrix and a few other things, not a volume file. > > On 10/8/18 5:28 PM, Frehiwot Woldeyes wrote: > > External Email - Use Caution > > Hello Freesurfers, > > I was attempting to reconstruct a monkey brain, i encountered an error during > talairach registration step, i have used tkregister2 to manually edit the > registration but i have gotten error there too: > > tkregister2 --targ > /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii --mov > /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii --reg > /usr/local/freesurfer/subjects/A004_crop.mhd.nii > tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl > target volume /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii > movable volume /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii > reg file /usr/local/freesurfer/subjects/A004_crop.mhd.nii > LoadVol 1 > ZeroCRAS 0 > $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ > Diagnostic Level -1 > regio_read_register(): No such file or directory > Could not open /usr/local/freesurfer/subjects/A004_crop.mhd.nii > ERROR: reading /usr/local/freesurfer/subjects/A004_crop.mhd.nii > > Do you have any thoughts on how to troubleshoot this one? > > Regards, > frehiwot > > > > _______________________________________________ > 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/20181009/72e4ebf3/attachment-0001.html > > ------------------------------ > > Message: 19 > Date: Tue, 9 Oct 2018 14:10:26 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Recon-all with/without T2 give the same > stats > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <d83c8c2f-a299-aabb-8d89-a34d14311...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > But are the lh.thickness files the same or different? > > On 10/9/18 1:46 AM, Jianzhong Chen wrote: > > External Email - Use Caution > > Hi Dr. Greve, > > I checked the lh.aparc.stats and rh.aparc.stats, the thicknesses (and the > other measures like volume and area) are all the same. > > Thanks, > Jianzhong > > Greve, Douglas N.,Ph.D. > <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> ?2018?10?9??? > ??10:16??? > The aseg.stats should be the same since that does not make reference to the > surfaces. The aparc stats should have been different because the thickness > should have been different. Can you check whether the thickness files are > different? > > On 10/8/18 9:39 AM, Jianzhong Chen wrote: > > External Email - Use Caution > > Dear All, > > I tried recon-all with/without T2 image using FS 5.3.0. Then I found that the > aseg stats and aparc stats with/without T2 are exactly the same. When I check > the pial surfaces, I can see that they are very similar but not the same. So > is it reasonable to see exactly the same stats? > An example of the pial surfaces with/without T2 is attached here. The red > line is lh.pial with T2 and the yellow line is the lh.pial without T2 > My command for recon-all with T2 is: recon-all -s ${subject} -i T1.nii -all > -T2 T2.nii -T2pial -sd ${T2_dir} > My command for recon-all without T2 is: recon-all -s ${subject} -i T1.nii > -all -sd ${T1_dir} > > Thanks, > Jianzhong > > > > _______________________________________________ > 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 > > > > _______________________________________________ > 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/20181009/f4317538/attachment-0001.html > > ------------------------------ > > Message: 20 > Date: Tue, 9 Oct 2018 10:56:45 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] very bad result using "mris_ca_train" and > "mris_ca_label" > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.20.1810091056030.20...@gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-15" > > Hi Maedeh > > the surface file should be the one that defines the common coordinate > system (usually sphere.reg) and the annotation should refer to a file in > the subject's label dir. Every subject in your list must have both files. > > cheers > Bruce > > On Tue, 9 Oct 2018, Maedeh Khalilian wrote: > >> ????????External Email - Use Caution???????? >> >> Dear Dr.Bruce Fischl >> Thank you very much for your great sense of responsibility. >> Sure, i have sent you a zip file named "Maedeh_results"(it was a rather big >> sized one so i had to >> send it through Wetranser). Hope you have received it. >> However, a general question is that, according to freesurfer help the >> required arguments for >> "mris_ca_train" are : >> mris_ca_train [options] <hemi> <canon surf> <annot file> <subject 1> >> <subject 2> ... <output file> >> >> as it seems it gets one surf file(e.g sphere.reg),and one annotation file, >> but several subjects...so >> what does this surface file refer to?should i make an average of all >> subjects' .reg files? and also >> for the annotation file ! just one .annot is enough or i have to make an >> average of several >> annotation files? >> if yes, how should i do that? >> i would be grateful if you could help me. >> Best regards >> Maedeh, >> ? >> >> > ------------------------------ > > Message: 21 > Date: Tue, 9 Oct 2018 15:50:09 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Extract individual vertex thickness values > from cortical parcellations > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <17d31e6c-d299-785a-758e-cf2d9e676...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > You can use matlab. read_curv.m will read in a thickness. > read_annotation.m will read in the annotation. Look at the help in both > for more info > > On 10/06/2018 11:36 AM, lindsay hanford wrote: >> ????????External Email - Use Caution >> >> Hello Freesurfer Community, >> >> I am looking for a way to extract thickness values at the level of >> each vertex from Freesurfer atlas-based parcellated regions >> (aparc.annot), or more generally lobes. Is this possible? >> >> Using mri_segstats I know it is possible to get more general metrics >> such as min, max and average thickness values, and # of voxels. Is it >> possible to use an annot file to read out the raw thickness values? >> >> This post was the closest I could find to answering my question, >> however, this was at the group level and not specified for parcellated >> regions. >> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022097.html >> >> Thank you in?advance, >> >> Lindsay >> >> -- >> *Lindsay Hanford, PhD* >> *The Buckner Laboratory**|**Harvard University* >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > Message: 22 > Date: Tue, 9 Oct 2018 15:56:28 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] nu_correct disk i/o issues > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <e745102a-6feb-e5eb-5c1c-1203c5a44...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > BTW, this should not be a problem in the next version > > On 10/07/2018 08:29 AM, Jasper van den Bosch wrote: >> >> Michael, I can't thank you enough. >> >> Knowing that it writes to /tmp made all the?difference. >> In my case I mounted an external directory on /tmp instead of the >> sessiondir approach, but it now runs fine. >> Jasper >> >> On Fri, 5 Oct 2018 at 23:47, Michael Krause <kra...@mpib-berlin.mpg.de >> <mailto:kra...@mpib-berlin.mpg.de>> wrote: >> >> Dear *, >> >> we also run Freesurfer on a cluster and are starting to use >> singularity, so >> naturally I'm curious about this issue. >> >> I was able to reproduce the error with a clean singularity run (-c >> -e). >> Then, I rebuilt a container to start nu_correct with "strace -f -e >> open,write" and I believe I found the problem: >> >> [pid 35994] >> open("/subs/testsub/mri/tmp.mri_nu_correct.mni.35410/nu1.imp", >> O_RDONLY) = 3 >> [pid 35994] open("/tmp/minc-qKdMD4", O_RDWR|O_CREAT|O_EXCL, 0600) = 5 >> [pid 35994] open("/tmp/minc-qKdMD4", O_RDWR|O_CREAT|O_TRUNC, 0666) = 5 >> [pid 35994] write(5, "\0\0\0\0\0\0\0\0", 8) = 8 >> [pid 35994] write(5, >> "CDF\1\0\0\0\0\0\0\0\n\0\0\0\3\0\0\0\6xspace\0\0\0\0\1\0"..., >> 8192) = 8192 >> [pid 35994] write(5, >> >> "|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0"..., >> 8192) = 8192 >> [...] >> [pid 35994] write(5, >> >> "|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0"..., >> 8192) = -1 ENOSPC (No space left on device) >> [pid 35994] write(2, "ncendef: ", 9ncendef: )? ? = 9 >> [pid 35994] write(2, "ncid 5", 6ncid 5)? ? ? ?= 6 >> [pid 35994] write(2, ": No space left on device", 25: No space left on >> device) = 25 >> >> >> So there are two issues here I think: >> >> 1) nu_correct is saving things to /tmp when it could just use ./tmp >> 2) the singularity default for "sessiondir max size" is 16MB, >> which includes >> /tmp, is too small for the minc-tmp files >> >> I changed the value from 16 to 1024 and it passed the nu_correct step. >> >> cheers, >> Michael >> >> On 10/5/18 5:57 PM, Greve, Douglas N.,Ph.D. wrote: >> > Not that I know of, but this is not a native FS script, it comes >> from the >> > MNI, so it could be doing something we don't understand. Can you >> do an >> > experiment for us? Can you run it outside of the container using >> reprozip >> > (or something equivalent) to see all the files it touches? >> > >> > On 10/5/18 5:31 AM, Jasper van den Bosch wrote: >> >> >> >> ????????External Email - Use Caution >> >> >> >> We are trying to run recon_all inside an fmriprep singularity >> container, >> >> but are running into an issue with nu_correct. It says it >> cannot write to >> >> disk, however there is plenty of space on the tmpdir and output >> dir. Does >> >> this script try to write to any other locations? Because this >> would fail >> >> inside the container, where each writable location has to be >> 'mounted'. >> >> >> >> Error message: >> >> >> >> ncendef: ncid 5: No space left on device >> >> Error outputting volume: possibly disk full? >> >> nu_evaluate: crashed while running evaluate_field (termination >> status=139) >> >> nu_correct: crashed while running nu_evaluate (termination >> status=65280) >> >> ERROR: nu_correct >> >> >> >> Command ran: >> >> >> >> nu_correct -clobber ./tmp.mri_nu_correct.mni.1121/nu0.mnc >> >> ./tmp.mri_nu_correct.mni.1121/nu1.mnc -tmpdir >> >> ./tmp.mri_nu_correct.mni.1121/0/ -iterations 1000 -distance 50 >> >> [xxx@yyyy.cluster:/data/BIDS/derivatives/freesurfer/sub-1/mri/] >> >> [2018-10-04 14:59:29] running: >> >> ? /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log >> -sharpen 0.15 >> >> 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask >> -nonotify -b_spline >> >> 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir >> >> ./tmp.mri_nu_correct.mni.1121/0/ >> ./tmp.mri_nu_correct.mni.1121/nu0.mnc >> >> ./tmp.mri_nu_correct.mni.1121/nu1.imp >> >> >> >> >> >> this issue at the fmriprep >> >> repo: https://github.com/poldracklab/fmriprep/issues/1308 >> >> possibly related: >> https://github.com/freesurfer/freesurfer/issues/462 >> >> >> >> Many thanks for any advice, >> >> Jasper van den Bosch >> >> >> >> >> >> >> >> _______________________________________________ >> >> 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 >> > >> >> ????????External Email - Use Caution >> >> _______________________________________________ >> 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 >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > Message: 23 > Date: Tue, 9 Oct 2018 15:57:26 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] masking cortical thickness > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <2f6d260e-9d6a-4839-6b96-ea63b4a46...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Use the --outmask option > > On 10/07/2018 08:59 AM, N Saf wrote: >> ????????External Email - Use Caution >> >> Dear Douglos, >> >> I did not understand how to use mri_label2label with the mask >> option(there is srcmask options not mask alone !). I extract my labels >> and as you explained I wanted to create i.e. binary mask of >> rh.fusiform.label? with mri_label2label : >> ? mri_label2label? --srcsubject case1 --srclabel rh.fusiform.label >> --trgsubject case1 --trglabel outputlabel.mgh --regmethod surface >> --hemi rh >> >> but it creats another label file not binary with mgh format I did not >> get how can I create mybinary.mgh mask in order to use in third >> command "mri_binarize --i lh.thickness --mask youmask.mgh --o >> lh.thickness.masked.mgh" >> >> would you please help me with this, it would be a great favor. >> >> Best regards, >> Nazanin >> >> On Mon, Jul 30, 2018 at 10:59 PM Douglas N. Greve >> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: >> >> Yes, that should work. You can create a mask by breaking the >> annotation >> into labels (mri_annotation2label), then converting the label into a >> binary mask (mri_label2label with --mask option), then >> mri_binarize --i >> lh.thickness --mask youmask.mgh --o lh.thickness.masked.mgh >> >> >> On 07/30/2018 01:47 AM, N Saf wrote: >> > >> > ????????External Email - Use Caution >> > >> > Dear Freesurfer Experts, >> > >> > I wonder how can I show the?cortical thickness surface on just one >> > region of my interest in Freeview.? assume that I want to see the >> > thickness surface of one of the regions in DKTatlas. does it >> work if I >> > make a binary mask of that specific region on >> aparcDKTatlas.annot and >> > then multiply it to the ?h.thickness surface ?? any help will be >> > appreciated. >> > >> > Best Regards, >> > Nazanin >> > >> > >> > _______________________________________________ >> > 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. >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 176, Issue 9 > ****************************************** > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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