Freesurfer July 2020

freesurfer@nmr.mgh.harvard.edu

96 participants
160 discussions

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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output of mri_surf2vol looks fragmented
by Sam W 08 Jul '20

08 Jul '20

External Email - Use Caution Hi, I'm trying to understand mri_surf2vol and mri_vol2surf but I'm not able to get the expected output when converting a surface back to volume. These are the commands I'm using: mri_vol2surf --mov lh_fusiform_pre.nii.gz --ref mri/orig.mgz --regheader sub01 --o lh_fusiform.gii --hemi lh mri_surf2vol --o lh_fusiform_post.nii.gz --subject sub01 --so surf/lh.white lh_fusiform.gii shouldn't lh_fusiform_pre and lh_fusiform_post look the same? lh_fusiform_post looks fragmented. Best regards, Sam

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Alternative Cerebellum parcellations
by Álvaro Deleglise 08 Jul '20

08 Jul '20

External Email - Use Caution Hello people! I was wondering how can I run a parcellation of the cerebellum with a different strategy than the one provided by the default subcortical segmentation (which only differentiates lh and rh white and grey matter). I'm currently analyzing longitudinal data from a motor learning experiment in which the cerebellum it's very important, so I would like to have more cerebellar ROIs. There are some papers that propose alternative parcellation strategies, and I recently found an article by Makris et al., 2003, *Human Cerebellum- Surface-Assisted Cortical Parcellation and Volumetry with Magnetic Resonance Imaging,* but I'm not sure if there is any implementation of any of these parcellations to perform in FreeSurfer. Does anybody already tried to do something similar? Or if there is another segmentation strategies available or more adequate and where can I find the necessary files? Thanks in advance.

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Re: [Freesurfer] Updating submillimeter data from 5.3 to 7.1 with -hires?
by Daniel Westfall 08 Jul '20

08 Jul '20

External Email - Use Caution Hi Douglas, It looks like the previous processing used 'recon-all -all -norm2-b 20 -norm2-n 5 -no-isrunning', this was from 2012 so I referenced the recon-all.log for this info. According to the log the original data was 0.9 mm size and then confirmed to 1 mm size. My hypotheses are specific to thickness (whole brain and ROIs based on the Yeo 7-network parcellation). So, basically I am trying to determine if I should convert to the -hires pipeline to take advantage of the submillimeter pipeline to get a more accurate representation of the cortical thickness. Or if using the previously processed 5.3 1mm conformed scan is fine. The cost/benefit really just alludes to the amount of time it will take to QC ~600 scans if I re-run in 7.1. If there is a huge advantage of switching to the -hires pipeline for cortical thickness measures then that is something I can move forward with. Thank you ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Wednesday, July 8, 2020 12:00 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 197, Issue 16 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.… 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: Updating submillimeter data from 5.3 to 7.1 with -hires? (Douglas N. Greve) 2. Re: Freesurfer Hippocampal Subfield Misalignment (Jenna Katherine Blujus) ---------------------------------------------------------------------- Message: 1 Date: Wed, 8 Jul 2020 11:15:56 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Updating submillimeter data from 5.3 to 7.1 with -hires? To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <8f7a8545-49e3-4a51-575f-3caa60db80e0(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" How did you do the 5.3 analysis? in 1mm/conformed space? And what are you hoping to accomplish by running it in v7.1 with -hires? On 7/8/2020 10:46 AM, Daniel Westfall wrote: > > ????????External Email - Use Caution > > Hi Everyone, > > I have access to two large datasets (~600 scans) that were previously > collected, processed, QC'd, and manually edited where necessary in > Freesurfer 5.3 with recon-all. However, the data is 0.9 mm isotropic > collected in a 3T scanner. I am attempting to decide if the > cost/benefit is worth switching the pipeline to Freesurfer 7.1 with > the -hires flag? The processing time is not the issue, mainly redoing > QC and manual corrections is the concern. > > 1. To publish 0.9 isotropic is it necessary to use the -hires pipeline? > 2. Is it appropriate to apply corrections calculated in the > Freesurfer 5.3 standard pipeline to Freesurfer 7.1 -hires (and > double check). Or do the manual QCs need to be completed from the > ground up? > 3. With the other 2 questions in mind, is it better to just go ahead > and convert the data to Freesurfer 7.1 -hires? > > Thank you, > Daniel > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.…

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

08 Jul '20

Hi! I meant that if the hippocampus was oversegmented (e.g., over the amygdala), you’d still have to paint new labels in those regions (as amygdala, in our example). You could use the Matlab functions under $FREESURFER_HOME/matlab (in particular MRIread and MRIwrite) to programmatically move the edits from aseg.mgz to wmparc.mgz. Cheers, /E 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 11:37 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, 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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Freesurfer July 2020