Freesurfer

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30088 discussions

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

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,

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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

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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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Re: [Freesurfer] Error running setup_configure
by Hoopes, Andrew 05 Oct '18

05 Oct '18

You’re attempting to build the dev version of freesurfer, in which case you should follow the build instructions on this page - https://surfer.nmr.mgh.harvard.edu/fswiki/BuildGuide. If you’d like to build freesurfer 6, you’ll have to checkout the "stable6" git branch before running setup_configure. Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Jennewein, Douglas M" <Doug.Jennewein(a)usd.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, October 5, 2018 at 2:07 PM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Error running setup_configure External Email - Use Caution We are attempting to build Freesurfer 6 on CentOS 7 x76_64. After cloning the git repo we see the following when running ./setup_configure configure.in:3866: the top level Makefile.am: error: required file './NEWS' not found Makefile.am: error: required file './AUTHORS' not found Makefile.am: error: required file './ChangeLog' not found automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' Makefile.am:27: error: required directory ./mri_warp_concat does not exist The folder mri_warp_concat/ does not exist in the cloned directory, and does not appear to exist in the github repo online<https://github.com/freesurfer/freesurfer> either. How can we build Freesurfer 6 from source on CentOS 7? Thank you Doug Jennewein

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Error running setup_configure
by Jennewein, Douglas M 05 Oct '18

05 Oct '18

External Email - Use Caution We are attempting to build Freesurfer 6 on CentOS 7 x76_64. After cloning the git repo we see the following when running ./setup_configure configure.in:3866: the top level Makefile.am: error: required file './NEWS' not found Makefile.am: error: required file './AUTHORS' not found Makefile.am: error: required file './ChangeLog' not found automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' Makefile.am:27: error: required directory ./mri_warp_concat does not exist The folder mri_warp_concat/ does not exist in the cloned directory, and does not appear to exist in the github repo online<https://github.com/freesurfer/freesurfer> either. How can we build Freesurfer 6 from source on CentOS 7? Thank you Doug Jennewein

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How to convert enhanced dicom format
by Craggs, Jason G. 05 Oct '18

05 Oct '18

External Email - Use Caution Greeting, Our radiology department recently installed a Siemens Vida system. It apparently exports in "enhanced dicom” format, which doesn't work with any of my software. Does anyone know anything about this format? Cheers, Jason

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QAtools for Freesurfer version6?
by Lee, Seonjoo 05 Oct '18

05 Oct '18

External Email - Use Caution I tired to use QA tools for freesurfer version6, but did not have much success. Is anyone know how to tweak QA tools for freesurfer version 6? Thank you. -Seonjoo Lee

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