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30132 discussions

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

2 1

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

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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

2 1

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

2 1

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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Morphing Buckner2011 MNI152 to subject's space {Disarmed}
by Peled, Noam 05 Oct '18

05 Oct '18

Dear group, I'm trying to morph the Buckner2011<http://www.freesurfer.net/fswiki/CerebellumParcellation_Buckner2011> cerebellum segmentation map from MNI152 to subject's space: mri_vol2vol --mov subjects/sub01/mri/norm.mgz --s sub01 --targ Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --m3z talairach.m3z --o sub01_Buckner2011_atlas_17_loose.nii.gz --nearest --inv-morph It worked with the 17 networks, but didn't work with the 7 networks version. Any ideas? This is really strange. Thanks, Noam

3 3

Definition of circular label centered on peak vertex
by Milde, Christopher 05 Oct '18

05 Oct '18

External Email - Use Caution Dear FS experts I`m interested in extracting beta values from a FSFAST analysis performed in the subject`s native space. The beta values shall be extracted from a circular label around the peak vertex. How can you define a circular label centered on the peak to extract average stats (e.g. betas) from that label? I`m aware how to create mask from the whole clusters in a given ROI saving them as labels and extracting stats. However I`m not sure how to define a circular mask or label. Thanks in advance Chris

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