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
