Freesurfer October 2018

freesurfer@nmr.mgh.harvard.edu

113 participants
156 discussions

FW: RE: error glm-fit-sim
by Caroline Beelen 08 Oct '18

08 Oct '18

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." <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> Subject: Re: [Freesurfer] error glm-fit-sim To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <504d6069-399f-163d-39a9-dcc6c02d32f9(a)mgh.harvard.edu<mailto:504d6069-399f-163d-39a9-dcc6c02d32f9@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

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Difference between 6.0.1 and 6.0.0
by Haakon Ramsland Hol 08 Oct '18

08 Oct '18

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.

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hippocampal subfields
by Marcel Heers 08 Oct '18

08 Oct '18

External Email - Use Caution Dear Eugenio, there is one error in the error.log: 'Could not set locale'. Best regards Marcel

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Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab
by Pradeep 08 Oct '18

08 Oct '18

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

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output values of vertices on surface into a textfile
by Sims, Sara A 08 Oct '18

08 Oct '18

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

3 4

very bad result using "mris_ca_train" and "mris_ca_label"
by Maedeh Khalilian 08 Oct '18

08 Oct '18

External Email - Use Caution Dear Freesurfer experts, I am using "mris_divide_parcellation" in order to increase the region numbers of Freesurfer parcellation output using "recon-all". e.g i have a 200-region parcellation.Now i wanna use "mris_ca_train" and this .annot file as an input to create an atlas file(.gcs). The code i run and the results on the terminal are : $ mris_ca_train lh sphere.reg LDestrieux200 test1 $SUBJECTS_DIR/test1/label/lh.Destrieux200.gcs computing means for 1 subject processing subject test1, 1 of 1... reading colortable from annotation file... colortable with 261 entries read (originally none) 4210 classifier means computed, 1.6/vertex, 0.5 priors/vertex computing covariances for 1 subject processing subject test1, 1 of 1... reading colortable from annotation file... colortable with 261 entries read (originally none) 75009 holes filled in class prior array 0 holes filled in gcsan array writing classifier array to /home/user/Desktop/Maedeh/test1/label/lh.Destrieux200.gcs... classifier array training took 0 minutes and 4 seconds. the problem is that when i use "lh.Destrieux200.gcs" and "mris_ca_label" to create an annotation file, the result i have is kinda awful !! and when i check it by tksurfer , the parcellation is not complete and i just see few regions...i dunno where i am making a mistake. the code and the results on terminal are : mris_ca_label test1 lh sphere.reg lh.Destrieux200.gcs $SUBJECTS_DIR/test1/label/lh.myDestrieux200.annot $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from lh.Destrieux200.gcs... average std = 0.2 using min determinant for regularization = 0.000 0 singular and 570 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 479 changed, 114679 examined... 001: 18 changed, 2844 examined... 002: 1 changed, 89 examined... 003: 0 changed, 5 examined... 000: 241 total segments, 38 labels (248 vertices) changed 001: 203 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) writing output to /home/user/Desktop/Maedeh/test1/label/lh.myDestrieux200.annot... classification took 0 minutes and 3 seconds. I would be grateful if u could help me. Cheers, Maedeh,

2 1

recon-all -make all error
by Dev vasu 07 Oct '18

07 Oct '18

External Email - Use Caution Dear all, I am encountering following error whenever i re-rerun my recon-all on cluster,,although i have downloaded new development version of recon-all.makefile, this error persists,kindly let me know what i am doing wrong recon-all -make all -s /home/hpc/u7x32/ru37veh2/emilie_struc/HC13 -sd /home/hpc/u7x32/ru37veh2/emilie_struc/new_recon ---------------------------------------------------------- recon-all -make all -s /home/hpc/u7x32/ru37veh2/emilie_struc/HC13 -sd /home/hpc/u7x32/ru37veh2/emilie_struc/new_recon /home/hpc/u7x32/ru37veh2/freesurfer_dev/bin/recon-all.makefile:195: recipe for target '/home/hpc/u7x32/ru37veh2/emilie_struc/new_recon/HC13/surf/lh.white.preaparc' failed recon-all -make all -s /home/hpc/u7x32/ru37veh2/emilie_struc/HC13 -sd /home/hpc/u7x32/ru37veh2/emilie_struc/new_recon make: *** [/home/hpc/u7x32/ru37veh2/emilie_struc/new_recon/HC13/surf/lh.white.preaparc] Error 1 Thanks Vasudev

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FreeSurfer update
by Dongsheng Wu 06 Oct '18

06 Oct '18

External Email - Use Caution Dear experts, Could the longitudinal statistics be processed in the version 5.3?How to update the version 5.3 to 6.0? Best regards, WU

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very bad result using "mris_ca_train" and "mris_ca_label"
by Maedeh Khalilian 06 Oct '18

06 Oct '18

1 0

Re: [Freesurfer] Freesurfer Digest, Vol 176, Issue 4
by Marcel Heers 06 Oct '18

06 Oct '18

External Email - Use Caution Dear Eugenio, there is one error in the error.log: 'Could not set locale'. Best regards Marcel On Thu, Oct 4, 2018 at 6:01 PM <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)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-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: output values of vertices on surface into a textfile > (Greve, Douglas N.,Ph.D.) > 2. hippocampal subfields error (Marcel Heers) > 3. Re: hippocampal subfields error (Iglesias Gonzalez, Eugenio) > 4. Mac OS free surfer instalation (Vasile, Eduard) (Vasile, Eduard) > 5. Re: Mac OS free surfer instalation (Vasile, Eduard) > (Dicamillo, Robert) > 6. mri_surf2surf --mapmethod nnf not working? (Viessmann, Olivia M.) > 7. create label from cluster obtained with mri_glm-fit-sim (Ting Li) > 8. Re: create label from cluster obtained with mri_glm-fit-sim > (Ting Li) > 9. Re: create label from cluster obtained with mri_glm-fit-sim > (Ting Li) > 10. Re: mri_surf2surf --mapmethod nnf not working? > (Greve, Douglas N.,Ph.D.) > 11. Problem with new tool on thalamus segmentation > (stdp82(a)virgilio.it) > 12. Re: mri_surf2surf --mapmethod nnf not working? > (Viessmann, Olivia M.) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 3 Oct 2018 17:09:32 +0000 > From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] output values of vertices on surface into a > textfile > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <e6681419-a7f2-cf18-fd5b-3f5455ce8236(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > 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(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ------------------------------ > > Message: 2 > Date: Wed, 3 Oct 2018 21:09:55 +0200 > From: Marcel Heers <marcel.heers(a)gmail.com> > Subject: [Freesurfer] hippocampal subfields error > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > < > CAMq9WnM7pRzZmGYA6PhxKa8GHPgrZraA_4sBspBOzOc9qjV5fQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Dear Eugenio, > > I am currently testing the newest version of your hippocampal subfield > analysis script. If I process the data on my macbook the files > hipposubfields.lh.T2.v21.file_ID contain the volumes of the different > nuclei, but on the linux server these files remain empty. On the server I > installed freesurfer as local user. Do you have any suggestions how to > check what might go wrong? > > Thanks for your help! > > Marcel >

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Freesurfer October 2018