Freesurfer

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30086 discussions

QAtools with Freesurfer version 6.0
by Wakim, Kathryn-Mary 09 Jul '20

09 Jul '20

External Email - Use Caution Hi all, I’m relatively new to Freesurfer, and I am just beginning to check the output of my recon-alls using QAtools. However, I’m running into a number of difficulties and errors with QAtools, and I’m wondering if this tool is not yet optimized for the current version of Freesurfer. I have attached the recon_checker.All.summary.log output from QA tools. Below, I’ve also highlighted some of the errors and issues I see in the recon_chcker log file. Please note thatt, per the subject’s recon-all log file, recon-all ran to completion with no errors. Overview of recon_checker errors: 1) ERROR: Subject 10201003 missing output file ../mri/nu_noneck.mgz * Note: this is repeated for a number of different output files 2) ERROR: Recon-all steps missing in subject 10201003 status file 3) View your snapshots by opening this file in an internet browser: * Note: I have attached a screenshot of the output .html file in-browser. Note that I have installed and verified installation of ImageMagick. Thank you very much for your help, Kamy Wakim

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(no subject)
by Peka Savayan 09 Jul '20

09 Jul '20

External Email - Use Caution Dear experts, I try to run recon-all using FS 7.1.0 on a cluster with OS CentOS6. I got the recon-all.log error message: ERROR: cannot find /share/apps/freesurfer-7.1.0/average/RB_all_2008-03-26.gca Thanks for your help. Sincerely, Peka -- Peka Christova Savayan, PhD Assistant Prof. Dept. Neuroscience Univ. Minnesota Member Center Cognitive Sciences Univ. Minnesota Graduate program Center Cognitive Sciences Univ. Minnesota Research Physicist Brain Sciences Center VAHCS

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Visualising atlas ROIs on inflated surface
by Leah Kelly 09 Jul '20

09 Jul '20

External Email - Use Caution Hello. Previously I have been able to visualise Desikan and Destrieux ROIs separately on a participant's inflated surface, as demonstrated below. I would like to be able to see more ROIs in this way but cannot remember how to do this. Would you be able to direct me to suitable guides (I could only find this on the website - https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI) or pass on an outline of the code needed to be able to do this? [image: image.png] Thank you in advance, Leah. PhD student in Cognitive Neuroscience and Neuroimaging Department of Psychology, University of York. Telephone 01904 322909

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Re: [Freesurfer] Question about 3T images and brain atlas compatibility
by Hye Min Shin 09 Jul '20

09 Jul '20

External Email - Use Caution Thank you for the response. Just to clarify, when you say as long as the surface reconstruction is correct do you mean that the surface should not have any gross defects and surfaces such as the pial surface show correct wm/gm boundaries? Best, Julia Shin ------------------------------------------------------------------------------- Date: Wed, 8 Jul 2020 11:13:50 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Question about 3T images and brain atlas compatibility To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <f5adfe37-3db5-9b5c-1ad7-3a1537996ee6(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" This is a surface-based atlas, so it is not sensitive to field strength as long as the surface reconstruction is correct because surfaces align with curvature and not intensity On 7/8/2020 12:39 AM, Hye Min Shin wrote: > > ????????External Email - Use Caution > > Hello, > > I wanted to extract brain morphometry data (cortical thickness, > surface areas, volume, etc) using PALS-B12 atlas. I have some 3T MRI > images that I have preprocessed using Freesurfer 3T flag. > > I am wondering if it would be ok to extract MRI data from 3T images on > atlases such as PALS-B12. How do we know whether certain atlases are > insensitive to field strength? > > Best, > Julia Shin > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] freeview 3.0
by fsbuild 09 Jul '20

09 Jul '20

External Email - Use Caution Hello Xiaomin, It might help for you to send along an example freeview command and file that demonstrates this issue in the WSL environment. - R. On Jul 8, 2020, at 12:08, Xiaomin Yue <yuexm(a)hotmail.com> wrote:        External Email - Use Caution        Dear all, The Freeview (3.0) coming with fs 7.1 can not show any surface brain (inflated, pial, white) in a solid color.  The Freeview is currently running under WSL and was running without a problem until I updated libXm4.  Is there a particular library file associated with libXm4  the Freeview needs to run without this problem? ThanksXiaomin_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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The thalamic atlas in MNI space
by 邹广源 09 Jul '20

09 Jul '20

External Email - Use Caution Dear experts I am performing a fMRI analysis about the thalamus. I would like to see the overlap of my thalamic ROI with the atlas derived in 'A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology' (Iglesias, NeuroImage, 2018). Is there a version of this atlas in the MNI space? I found the 'ThalamicNuclei' folder in FreeSurfer but it seems not an atlas in the MNI space. I am new in FreeSurfer. Could you please give me some suggestions? Thanks for your time. Best, Guangyuan Zou

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Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
by Iglesias Gonzalez, Juan E. 08 Jul '20

08 Jul '20

Just the subfields ;-) Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Jenna Katherine Blujus <jkblujus(a)uwm.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, July 8, 2020 at 18:11 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment External Email - Use Caution Hi Eugenio, Great, thank you! One last question - after I edit the aseg and wmparc files would you recommend that I only rerun the recon-all hippocampal-subfields-T2 step or should I rerun certain autorecon steps of recon-all? Thank you! Jenna Jenna K. Blujus, M.S. Graduate Student Neurobiology of Aging Laboratory University of Wisconsin-Milwaukee jkblujus(a)uwm.edu ________________________________ From: Jenna Katherine Blujus <jkblujus(a)uwm.edu> Sent: Wednesday, July 8, 2020 10:36 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: Freesurfer Hippocampal Subfield Misalignment Hi Eugenio, Thank you for the tips! This has happened to a number of my subjects but I have finished editing the HC label in their aseg files. How would I copy the HC from aseg.mgz to wmparc.mgz? Can you clarify what you mean by "you still need to fix the surrounding labels"? Thank you, Jenna Message: 3 Date: Tue, 7 Jul 2020 20:53:12 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <85489126-5DC1-4464-810B-01A7E825895A(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Dear Jenna, 1.Manually editing aseg.mgz fixes the initialization (super important). 2.Manually editing wmparc.mgz fixes the intensity priors (less important, but still important) If it?s only 1 subject in a bigger study, I?d probably call it a QC fail and leave it out. If it?s a single case you?re very interested in, I would edit both aseg.mgz and wmparc.mgz (you can copy the hippocampus from one into the other, but you still need to fix the surrounding labels). Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jeigle… Reply Forward Jenna K. Blujus, M.S. Graduate Student Neurobiology of Aging Laboratory University of Wisconsin-Milwaukee jkblujus(a)uwm.edu ________________________________ From: Jenna Katherine Blujus Sent: Tuesday, July 7, 2020 3:23 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Hippocampal Subfield Misalignment Hi Experts, I ran the hippocampal subfield segmentation protocol using a T2 image that does not cover the whole brain in Freesurfer v6.0. I noticed that the alignment of the ?h.hippoSfLabels-T2.v10 output to the anatomical boundaries of the hippocampus in some of my subjects is off. For example, the left hippocampal subfield segmentation in one subject is superior and medial to the hippocampus. I checked the aseg.presurf file (since I am using v6.0) and indeed the whole left hippocampus is off. I saw in a previous thread (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23942.html) that it was suggested to edit the hippocampal segmentation within the aseg file to potentially improve alignment of the subfield segmentation. However, a more recent post (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg54543.html) stated that both the wmparc.mgz and aseg.mgz files would need to be edited and that this was not recommended. Do you have any recommendations on how to move forward? I did edit the hippocampal segmentation within the aseg.presurf file in one of my subjects and reran the subfield segmentation command which substantially improved the output (i.e., it overlays on the hippocampus after correction). Would you suggest that I continue with editing the aseg using previously published protocols on segmenting the hippocampus by hand or would you recommend something else? Thanks in advance! Jenna

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Re: [Freesurfer] Freesurfer and singularity container (bash script)
by fsbuild 08 Jul '20

08 Jul '20

External Email - Use Caution Hello Ahmed, There is one error message indicating you are running out of disk space to write to.  Not clear to me if that is inside or outside the container, but either files need to be deleted and/or your disk partition needs to be larger. I would strongly discourage running as userid root.  Root has privileges that non-root users don’t have, so if something is not setup correctly privilege wise in the machine image, then you will not find out when running as root.   And once you run something as root, then non-root user may subsequently have issues running the same commands because they cannot delete/create temporary files previously created in subdirectories and/or owned by root, and commands as those non-root users will fail.   As part of building the container image (as root), it should be possible to create a normal non-root userid and then select that non-root userid to be the userid when the container runs (or at least that works in docker). - R. On Jul 8, 2020, at 16:37, Bahrani, Ahmed A. <ahmed..bahrani(a)uky.edu> wrote:        External Email - Use Caution        Hello, I have a question related to the singularity container to run a bash script that includes freesurfer commends. The issue isI have built a singularity container and included the freesurfer license in the container. Recalling and executing the script were run successfully as a root user login (without any errors), while as a general user (non-root) login, it showed an error with nu_correct; however, mri_convert seems to run fine as a step before nu_correct. The nu_correct used in the script four times. For the first to third nu_correct, it showed a full iteration (50/50) for each one and showed the following error:---Error message---evaluate_field: posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed.nu_evaluate: crashed while running evaluate_field (termination status=134)nu_correct: crashed while running nu_evaluate (termination status=65280)-------------------------------------------------------------------- Then, at the fourth  nu_correct it stopped after 48 iterations then showed the following error: ---Error message---ncvarput: ncid 4: No space left on devicemivarput1: MINC package entry pointnu_evaluate: crashed while running minccalc (termination status=768)nu_correct: crashed while running nu_evaluate (termination status=768)-------------------------------------------------------------------- Note: I am usingLinux Redhat 7.9 and the singularity installed using YUM command.Singularity version 3.6.0 For generating the container, I have used the following:singularity build -F xxx.sif xxx.def For running the container, I have used the following:singularity run -e -C -H /home/Ahmed/aaa/s:/opt/data xxx.sif bash /opt/s/s1_WMH.sh  Would you advise please, I want to run the container on other computers, but in this case, it will not work. Thanks,Ahmed_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer and singularity container (bash script)
by Bahrani, Ahmed A. 08 Jul '20

08 Jul '20

External Email - Use Caution Hello, I have a question related to the singularity container to run a bash script that includes freesurfer commends. The issue is I have built a singularity container and included the freesurfer license in the container. Recalling and executing the script were run successfully as a root user login (without any errors), while as a general user (non-root) login, it showed an error with nu_correct; however, mri_convert seems to run fine as a step before nu_correct. The nu_correct used in the script four times. For the first to third nu_correct, it showed a full iteration (50/50) for each one and showed the following error: ---Error message--- evaluate_field: posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed. nu_evaluate: crashed while running evaluate_field (termination status=134) nu_correct: crashed while running nu_evaluate (termination status=65280) -------------------------------------------------------------------- Then, at the fourth nu_correct it stopped after 48 iterations then showed the following error: ---Error message--- ncvarput: ncid 4: No space left on device mivarput1: MINC package entry point nu_evaluate: crashed while running minccalc (termination status=768) nu_correct: crashed while running nu_evaluate (termination status=768) -------------------------------------------------------------------- Note: I am using Linux Redhat 7.9 and the singularity installed using YUM command. Singularity version 3.6.0 For generating the container, I have used the following: singularity build -F xxx.sif xxx.def For running the container, I have used the following: singularity run -e -C -H /home/Ahmed/aaa/s:/opt/data xxx.sif bash /opt/s/s1_WMH.sh Would you advise please, I want to run the container on other computers, but in this case, it will not work. Thanks, Ahmed

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white vs pial target surface
by Sam W 08 Jul '20

08 Jul '20

External Email - Use Caution Hello, mri_vol2surf has the option to add a target surface (--surf) which can be the white (default) or pial surface. I get slightly different results depending on whether I use the white or pial surface as the target surface, so I was wondering in which situation should I use the white over the pial surface? Best regards, Sam

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Freesurfer