Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Synthsr
by Castro Leal, Gonzalo 14 Oct '21

14 Oct '21

External Email - Use Caution Hello FreeSurfer, I am trying to run the following comand: :~$ synthsr --i $SUBJECTS_DIR/super_resolve/ --o $SUBJECTS_DIR/super_resolved/ --ct --threads 4 --cpu synthsr: command not found Is this due to the synthsr being broken or with my installation of freesrufer developers edition? Many thanks, Gonzalo.

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Re: [Freesurfer] A question regarding a Freeview command (Douglas N. Greve) 8/10/21
by inbal paran 14 Oct '21

14 Oct '21

External Email - Use Caution Dear FreeSurfer developers, First, thank you Douglas very much for your reply. I have a follow up question, and for some reason I wasn't able to continue the thread, so I have copied the thread with Douglas's answer and my first question below. Here is my followup question: I did the ROI analysis, asegstats2table and mri_glmfit with --table option as you suggested, but the thing is that I want to visualize my significant results using Freeview, how can I do that? Also - by any chance can you tell me how can I continue the thread? When I am entered the archive I tried to click on "reply via email to.." but that just opens the outlook as a default and I don't work with outlook. For some reason I can't open the thread using gmail. Thank you very much, Best, Inbal Message: 7 Date: Fri, 8 Oct 2021 12:51:42 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] A question regarding a Freeview command To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <bd3f5853-edf3-270d-9d1e-8c6f65d55420(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" The volume is the volume of cortex only, not the volume of subcortical structures. We don't have a VBM-style analysis that would be needed for subcortical GM. You can always do an ROI analysis, asegstats2table and mri_glmfit with --table option; this will allow you to analyze the volume of each structure as a single number, not a map. To answer your question, your freeview command line does not need to change. On 10/4/2021 2:27 AM, inbal paran wrote: > > ????????External Email - Use Caution > > Dear FreeSurfer developers, > > I am trying to run a group analysis to test for an association between > *gray matter volume* and a behavioral measure of interest. > reacon-all ran OK for all my subjects as well as mris_preproc followed > by mri_surf2surf, and finally glmfit.? Finally, I wanted to visualize > the significant voxels using freeview and followed the command line in > the tutorial of the group analysis (*MailScanner has detected a > possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1vcxvE4KyDsi4qqXPfbLdF0-Ec-nWSe90uzyY86VVnWLhO… > < https://secure-web.cisco.com/1_d3qazq-_19W6y1XEkeVPINXH5vgktFtuM1FrpU_HJNr4… >). > However, since I am talking about volume and not surface, I wasn't > sure how to edit the final command to visualize my results in > freeview. I want to make sure it will include significant voxels both > in subcortical + cortical regions. Should I use a stats.table file as > an input? As you probably understand, working with Linux and > FreeSurfer are both very new to me, if it's possible, any help would > be greatly appreciated. > > If it's relevant, these are the details of the version and platform > I'm using: > 1) FreeSurfer version: > freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 > 2) Platform: Ubuntu 20.04.1 LTS > 3) uname -a: Linux inbal-paran 5.11.0-37-generic #41~20.04.2-Ubuntu > SMP Fri Sep 24 09:06:38 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux > 4) I also attached the mris_preproc log files in case it can help > > Kind regards, > Inbal Paran > > -- > *Inbal Paran, M.PT <http://secure-web.cisco.com/1_uWMvw0JQHDbRb3qSmM-v2YM-E0oQrb6OCiSvXSQcDnOGy…> > < http://secure-web.cisco.com/1TCV1fAKzZJ5GOMgMi06jDdgf5mlDmrjtvqzBaNtTAOycuW… >. > * > Schwartz Movement analysis & Rehabilitation Laboratory, Physical > Therapy Department, Recanati School for Community Health Professions. > Faculty of Health Sciences at Ben-Gurion University of the Negev. > Thanks again for your help, Inbal -- *Inbal Paran, M.PT <http://secure-web.cisco.com/1GATqktVB9GCv-D6rmlzLZKLrLOjzGIDyvhTd6-WnB7r0cQ…>.* Schwartz Movement analysis & Rehabilitation Laboratory, Physical Therapy Department, Recanati School for Community Health Professions. Faculty of Health Sciences at Ben-Gurion University of the Negev.

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Segmentation of thalamic nuclei - misplaced position
by Edyta Leks 14 Oct '21

14 Oct '21

External Email - Use Caution Hi Freesurfer expert, I have a question regarding the segmentation of thalamic nuclei. I processed 15 subjects with freesurfer v6 (recon-all) and additionally, ran the thalamic segmentation implemented in FreeSurfer. Then, I wanted to use the label of the thalamic nuclei to select an ROI in the VM, VPL and in other nuclei to perform the ROI analysis in SPM. Therefore, I converted the outputs of the segmentation (ThalamicNuclei.v12.T1.mgz) into nifti files by using the command "mri_convert .mgz .nii". Additionally, using ImgCal in the SPM, I created a mask for each nuclei separately. Most nuclei look great and correspond to their anatomical position. Unfortunately, the position of some nuclei is completely wrong. For example, the size of the VM (left) is definitely too small and the position seems to be on the border / outside of thalamus (attached files and link). I do not see the right-VM at all. This issue affects all my data as well as data analyzed in another institute. In the attached picture (Thalamic_segmentation_VMleft.png), blue represents the VM. We can clearly see that the position as well as the size is completely incorrect compared to the known anatomical position or shown in your publication. Could I ask for an explanation and help in solving the problem. The parameter for T1 and T2 scans: T1: 208slices, voxel size=0.8mm isotropic, TE=3.16ms, TR=2400ms, BW=220Hz/px, ES=7.5ms T2: 208 slices, voxel size=0.8mm isotropic, TE=5.63ms, TR=3200ms, BW=744Hz/px, ES=3.52ms Here you can find all the files: https://secure-web.cisco.com/1KtaGTX0Nfx2jwZl-X1QkJstv6OQtmYKCMAYA5rzu-lXHK… Best regards, Edyta Leks Edyta Leks High Field MR Center Max Planck Institute for Biological Cybernetics Max-Planck-Ring 11 72076 Tübingen Germany ________________________________________________ office: 4.B.06 tel: +49 7071 601 918 e:mail: edyta.leks(a)tuebingen.mpg.de

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Re: [Freesurfer] Comparing volumes before and after editing, and aparc+aseg after rerunning recon-all
by Kang, Jee Won 13 Oct '21

13 Oct '21

External Email - Use Caution Thank you for your reply! It was very helpful. I was able to successfully create the difference mask according to your instruction. As far as the sum.dat output from mri_segstats, I'm uncertain as to what columns to look at to find the percent of each ROI that had edits; all I get is information regarding the number of voxels, and the mean, stdDev, min, max, and range of intensity for each structure. To provide some more context, the goal of this endeavor is to essentially create a sort of "log" of edits, to know the regions where voxels were erased or added (and to which volume). In terms of identifying only edited regions, would it be better to create a mask which extracts only voxels with a value of 1 or 255? Also, I had a question regarding a different topic with regards to to aparc+aseg.mgz after rerunning recon-all: although the pial surface changed after rerunning recon-all, the aparc+aseg.mgz didn't seem to change. I've attached a screenshot where you can see the aparc+aseg extending significantly beyond the pial surface, so I'm wondering why that might be, and whether it's a problem? In the troubleshooting slides it does mention that it's okay if the cortical ribbon extends beyond the surface, since the ribbon isn't used for anything, but why would it not change to reflect changes in the pial surface? Thank you very much again for your assistance. -Jee Won ________________________________________ Date: Fri, 8 Oct 2021 12:48:03 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Comparing volumes before and after editing To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <8558ace1-9ef4-a75c-984b-1b53cc87e2ea(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" If you subtract them, eg, fscalc vol1.mgz sub vol2.mgz abs gte 0.5 -o diff.mgz This command will subtract the two, take the absolute values, then threshold (binarize) the differences. I'm not sure what you are looking for in terms of aparc+aseg, but you can do something like mri_segstats --ctab-default --seg aparc+aseg.mgz --excludeid 0 --i diff.mgz --sum sum.dat and sum.dat will tell you the percent of each ROI that had edits On 10/1/2021 4:01 PM, Kang, Jee Won wrote: > > ????????External Email - Use Caution > > Hello all, > > > I'm very new to Freesurfer and have?started with quality-checking > recons. I wanted to know if there is a way to compare volumes before > and after edits were made before recon-all has been re-run. > > > For example, if we have brainmask.mgz that has been edited and > brainmask_ORIG.mgz before any edits were made, is there a way to > create?a volume overlay and extract the areas where edits were made > (perhaps parsed from aparc+aseg)? > > > Thank you for your assistance on this! > > > -Jee Won > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://secure-web.cisco.com/1tDN495Zmz69_tS_DgP3uRxsUNUoW4dfYipN6gNbM54T8s…

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IP Problems
by Alison McDonnell 13 Oct '21

13 Oct '21

External Email - Use Caution I was having some trouble with Freesurfer on a windows computer and was wondering if you had any ideas. I was able to download and install it but when I got to the end to run it I got the error message to do with the IP address, the same as the one shown in the screenshot below. The instructions said this could happen so wasn't worried and did what they said but the error happens every time I logout and log back in. The freeview program also doesn't actually run but seems to try to load and no errors come up when I try run it so I think I might just not be fixing the IP problem. [image: image.png]

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Re: [Freesurfer] Segmentation fault (core dumped) of freeview
by fsbuild 13 Oct '21

13 Oct '21

External Email - Use Caution Hello Yuhui, Did you try something like the following (from https://secure-web.cisco.com/1hub7Psr57JCR6YgoGWEJLmEuz6voF9O_4wwW1Ngq-Krek…) to set FREESURFER_HOME (?) and then after source'ing the shell setup script you should of seen output like ... $ export FREESURFER_HOME=/your_path_to/freesurfer/7.2.0$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-linux-centos8_x86_64-7.2.0-20210720-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /home/tester/freesurferFSFAST_HOME       /home/tester/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /home/tester/freesurfer/subjectsMNI_DIR           /home/tester/freesurfer/mni $ which freeview/your_path_to/freesurfer/7.2.0/freeview … set TUTORIAL_DATA … I would try just typing freeview on the command line to test that it brings up an empty window before trying to run any of the tutorial commands with it, $ freeview - R. On Oct 12, 2021, at 22:42, Yuhui LIANG 梁玉慧 <liangyuhui(a)westlake.edu.cn> wrote:        External Email - Use Caution                External Email - Use Caution        Hello,As a beginner, I am trying to run freeview -v using tutorial_data by the code below.freeview -v \good_output/mri/T1.mgz \good_output/mri/wm.mgz \good_output/mri/brainmask.mgz \good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \-f good_output/surf/lh.white:edgecolor=blue \good_output/surf/lh.pial:edgecolor=red \good_output/surf/rh.white:edgecolor=blue \good_output/surf/rh.pial:edgecolor=red I am getting an error :Segmentation fault (core dumped)but it did not produce CORE file. And I've downloaded the tutorial data set before begin and I am sure that set the TUTORIAL_DATA environment variable properly as specified on the tutorial data page. I am using freesurfer version 7.2.0 in CentOS 8. Any advice would be appreciated! Thanks, Yuhui_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1Thxeq5mfyjHL_ecNgfklwIAfLQXmU16VfwPdyUKAEKqI3tHHfJBOS99IgKieVMP1yJHqdMyYdM8YKNO41VpZxyy8QefzmhvAveAr7KCEFmfqRMhDCLZBp4cDP8V_Q9AhKdxDr5U0wEeEje5Nj9HXVy4Q3vemfAVWo1jwgjJTjbVzGuh82uuVinDziFut_t5uJ1e9nMgXnk2bHv7F49TbGgLvplUj2Bj7osfbpUAqQ0MYQZmw2rChHKEqez3A1ywYFPsmGYC3guJm5PmQ7h13lw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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Segmentation fault (core dumped) of freeview
by Yuhui LIANG 梁玉慧 12 Oct '21

12 Oct '21

External Email - Use Caution Hello, As a beginner, I am trying to run freeview -v using tutorial_data by the code below. freeview -v \ good_output/mri/T1.mgz \ good_output/mri/wm.mgz \ good_output/mri/brainmask.mgz \ good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f good_output/surf/lh.white:edgecolor=blue \ good_output/surf/lh.pial:edgecolor=red \ good_output/surf/rh.white:edgecolor=blue \ good_output/surf/rh.pial:edgecolor=red I am getting an error :Segmentation fault (core dumped) but it did not produce CORE file. And I've downloaded the tutorial data set<https://secure-web.cisco.com/1YhwP8bFwqbQw8ArjPIWKZBPJes6m8JxvN_roH8NEcnLfd…> before begin and I am sure that set the TUTORIAL_DATA environment variable properly as specified on the tutorial data page. I am using freesurfer version 7.2.0 in CentOS 8. Any advice would be appreciated! Thanks, Yuhui

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Open positions at The Ohio State University: Post-dococtoral Researcher, Psychometrician, & Study Coordinator
by Teng, James 11 Oct '21

11 Oct '21

External Email - Use Caution The Clinical Neuroscience Lab, in the Department of Psychology, within the College of Arts and Sciences, seeks a Post-Doctoral Researcher (R29059), a Psychometrician (R13824), and a Study Coodinator (29068) to join our team. The Clinical Neuroscience Lab is directed by Dr. Ruchika Prakash, and the laboratory is funded by the National Institute on Aging to conduct a randomized controlled trial of mindfulness meditation for older adults in the Columbus community. The lab recently received additional funding to increase the representation of Black, Indigenous, and/or People of Color in our clinical trial. We are excited to receive this funding, and we hope to find a candidate who is passionate about working with diverse communities and individuals. Apply online at: https://secure-web.cisco.com/11XZ7GSpquo2K34Cy2WyF2fIiLSV2uXiUNvLonCYJRP5v6… under the respective job listings Post-Doctoral Researcher (R29059), Psychometrician (R13824), and Study Coodinator (29068), and submit a CV, a brief statement of your research interests, your expected date of availability, and the names and contact information of three references. If you have questions about the position or the lab, please contact Dr. Ruchika Prakash at prakash.30(a)osu.edu. Lab Website: https://secure-web.cisco.com/1br5PNyboP4J53ZddAEBfrlv5QBGhIfyia8PupfmAqaxSL… To build a diverse workforce, The Ohio State University encourages applications from all individuals. Ohio State is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to age, race, color, religion, sex, sexual orientation, gender identity, national origin, disability status, or protected veteran status.

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error using mri_convert
by Rizzo, Nolan W 11 Oct '21

11 Oct '21

External Email - Use Caution Hello FreeSurfer developers, I am attempting to use mri_convert to convert DICOM files to a NIfTI file. The DICOM images were obtained from a Siemens 3T Prisma scanner with VE11C software version. When mri_convert is run to convert the .dcm files to .nii , an error occurs that displays "bad fd number". I believe the problem occurs when mri_convert is trying to decompress the new JPEG format of the DICOM files. I have listed the FreeSurfer version and OS that I used below. Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 Platform: Ubuntu 16.04 This error did not occur when running mri_convert on the Mac version of FreeSurfer using OS Mojave. The same DICOM files (as above) were used. mri_convert ran without error and produced the .nii file. Thank you.

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Question about fsaverage
by Dongyue Zhou 11 Oct '21

11 Oct '21

External Email - Use Caution Dear FreeSurfer experts: I use the 'qcache' command to get the file '$SUBJECTS_DIR/subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh'. I can get cortical thickness in each vertice by reading this file in matlab. And I know mean CT is computed by dividing sum CT of all ROI vertices by the number of ROI vertices. Is there any way I can get annot for this file in one sub?

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