Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30131 discussions

Re: [Freesurfer] SAMSEG "lesion" (Illegal instruction) ~ running VM_67
by fsbuild 26 Feb '22

26 Feb '22

External Email - Use Caution Hello Randy, I think the expectation is for users to run “samseg” from the command line.  (The samseg script is a front-end you run with command line options, e.g., —help, which calls samseg_run that in turn runs the samseg python scripts in the freesurfer python distribution which includes the tensorflow code). I can’t speak to the validity of the command + options causing the crash, but I would look too see if a “core” file was written in the directory where the command ran that produced the “Illegal instruction” error and subsequent crash.  The core file might also be under /var/crash.  If you have the core file you could name it something unique and try uploading it to https://secure-web.cisco.com/13zdjoSMY5sCPpxW673b6aDxUESbBUC7j-BF_P… someone to look at. - R. On Feb 24, 2022, at 11:58, daedalus39(a)aol.com wrote:        External Email - Use Caution        Following up on yesterday's email:I looked up the help text for SAMSEG on the VM (“run_samseg –help”).  The flag for --lesion indicates that Tensorflow is required.     --lesion        Enable lesion segmentation (requires tensorflow). I'm not sure is tensorflow is installed in VM_67, but "which tensorflow" returned nothing.  While my question only reported the “core dump” and a request to check the syntax, I did ask if the “lesion” flag was implemented in the VM.  If it's not installed in VM_67, would you be able to offer some guidance as to where the safest download site is and some suggestions as to how to install it?Sincerely,-Randy-----Original Message-----From: daedalus39(a)aol.comTo: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>Sent: Wed, Feb 23, 2022 1:19 pmSubject: SAMSEG "lesion" (Illegal instruction) ~ running VM_67Dear Experts,I am trying to test SAMSEG "lesion" on VM_67 and after I entered:run_samseg --input /home/developer/subjects_new/o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T30-acc_orig__S689126_I1001975.nii /home/developer/subjects_new/rT1_o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T2-FLAIR__S689135_I1001984.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /home/developer/subjects_new/Lesion-test/...I got the following errorIllegal instruction (core dumped)Is there anything glaringly wrong in my instruction/input phrase?Is SAMSEG "lesion" implemented in the new VM?  I was able to test the "basic" SAMSEG with a single T1 earlier this morning (it ran just fine)Thanks in advance for any help.-Randy_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Using mri_transform with output of bbregister
by Tisdall, Dylan 25 Feb '22

25 Feb '22

External Email - Use Caution Hi all, Thanks again for all the help so far with getting my data registered and surfaces extracted. I have one further issue that I'm hoping to get help with. I've used bbregister to align my T2 scan with the surfaces from my T1 scan. However, the output is resampled down to 1mm iso and a 256^3 volume; I'd like to keep the native 0.8 mm resolution and FOV if possible (acknowledging, of course, there's actually some blurring in the interpolation, but just for the sake of nominal consistency). I tried to work around this by applying the .lta output by bbregister to my T2 scan (with the goal of eventually using the --out-like flag to specify the sampling resolution, but not doing that yet): mri_transform T2_SPACE.nii.gz T2_SPACE_transform.lta T2_SPACE_warped.nii.gz However, when I load the resulting output volume (T2_SPACE_warped.nii.gz) in freeview, it has swapped axes. Strangely, this isn't the case with the output volume generated by bbregister... it's well-aligned with the surfaces. Similarly, if I load the T2_SPACE.nii.gz into freeview, and apply T2_SPACE_transform.lta as part of the load command, the volume is well-aligned. So what's different about how mri_transform applies that .lta file, compared to bbregister and freeview? Is there a way to just get bbregister to resample my T2 scan with the original resolution and FOV, so I can avoid applying mri_transform altogether? I don't see an --out-like option for bbregister, but is there a different flag? Thanks again, Dylan

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Neverending mris_fix_topology
by Peled, Noam 25 Feb '22

25 Feb '22

Dear group, I'm trying to run recon-all (freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551) on my Martinos' desktop. I killed it after waiting quite a of time for the mris_fix_topology to be completed: Waiting for PID 225967 of (225964 225967) to complete... What can I do to be able to process this subject? I attached the recon-all log. You can also find all the logs here: /autofs/space/mmvtclin_001/thibault/1/users/npeled/subjects/UN07/scripts Thanks! Noam

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PetSurfer: subcortical volume-based analysis
by Jennifer Bramen 25 Feb '22

25 Feb '22

External Email - Use Caution Dear Freesurfer Developers I am doing an ROI--based amyloid PET scan analysis. I have completed all of the steps from the PetSurfer wiki. I now have the preprocessed, averaged, resampled, smoothed PET data in MNI305 space which is constrained to the subcortical gray matter mask. How do I extract mean intensity within all of the subcortical ROI? Thank you! Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069

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NeuroImage: Reports: Call for papers for Special Issue on Replication findings in neuroimaging studies
by YAN Chao-Gan 25 Feb '22

25 Feb '22

External Email - Use Caution Replication is essential for progress in science. There are several reasons why findings may not replicate, including sampling variability, limited statistical power, cultural/population influences, and improvements in data acquisition and analysis methods. Replication studies are our best attempt at confirming or questioning the reliability of important findings. Replication studies also provide a crucial mechanism for reaching consensus about empirical support for or against a theory. Unfortunately, replication studies are difficult to publish, because many journals judge them as “lacking novelty.” For these reasons, we have created a special issue that highlights replication studies. We invite submissions that seek to replicate published neuroimaging studies, regardless of whether the initial results are confirmed. The primary criteria for acceptance are methodological and statistical rigor -- not conceptual novelty. Novel results are also welcomed, but authors must clearly state which analyses are replications and which are novel. Researchers may use their own collected data, original data from the to-be-replicated study, or publicly available data. We hope that this special issue will help highlight the importance of rigorous replication studies for ensuring progress in neuroimaging. *Submission instructions* The Neuroimage: Reports submission system is open for submissions to our Special Issue from *01 Oct 2021*. When submitting your manuscript please select the article type “*VSI: Replication*”. Please submit your manuscript before *01 Mar 2022.* All submissions deemed suitable to be sent for peer review will be reviewed by at least two independent reviewers. Once your manuscript is accepted, it will go into production, and will be simultaneously published in the current regular issue and pulled into the online Special Issue. Articles from this Special Issue will appear in different regular issues of the journal, though they will be clearly marked and branded as Special Issue articles. Please see an example here: https://secure-web.cisco.com/1CJkKxcFEBPguyPfb5m0Yr2MoiAzErZw3HYZKhuEAMSHET… Please ensure you read the Guide for Authors before writing your manuscript. The Guide for Authors and link to submit your manuscript is available on the Journal’s homepage at: https://secure-web.cisco.com/1VSgggrvcDPky-89wNR6lcPY0XqXuCfOZAX-r7Wa1HcuPp… Inquiries, including questions about appropriate topics, may be sent electronically to Dr. Yan Chao-Gan (ycg.yan(a)gmail.com) Best, Chao-Gan -- Chao-Gan YAN, Ph.D. Professor, Principal Investigator Director, International Big-Data Center for Depression Research Director, Magnetic Resonance Imaging Research Center Institute of Psychology, Chinese Academy of Sciences 16 Lincui Road, Chaoyang District, Beijing 100101, China - Initiator <http://secure-web.cisco.com/1sqIAAZ4sZdTTXMKfxT5Aar2JR-7UiWQN4aQSU7ygjFTldr…>DPABI <http://secure-web.cisco.com/1oInECTabhfK3d2rurp29HORgmXMA7sq2SIDskuFNuKnDgO…> <http://secure-web.cisco.com/1sqIAAZ4sZdTTXMKfxT5Aar2JR-7UiWQN4aQSU7ygjFTldr…>, DPABISurf, <http://secure-web.cisco.com/1XPTEW4lBFtrlvcsygGbgiVdlAQ26ae4_S7nefApkjEds0k…>DPARSF <http://secure-web.cisco.com/1sqIAAZ4sZdTTXMKfxT5Aar2JR-7UiWQN4aQSU7ygjFTldr…>, and The R-fMRI Network <http://secure-web.cisco.com/1TCtydiq5Yh8xn1WXFHq0xSYHUMfBiOaJiSlkzkVhdXs_ms…> ( RFMRI.ORG <http://secure-web.cisco.com/1Y_OweFD7n8m7sSc_adhdgF-QyZ2_4q16Hw2t4tYSmw0HA2…>) http://secure-web.cisco.com/1p7GiR8RwAPykrvrU-kv5cEmnIMwRR95RSJmBn47-AcsD64… http://secure-web.cisco.com/1wC4UpbExTFsWuXE3IWRwjCjcBW1uPj-8MrNX4mlQzLH_o7…

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Re: [Freesurfer] Ubuntu VM password
by fsbuild 25 Feb '22

25 Feb '22

External Email - Use Caution Sending the info to your email shortly. - R. On Feb 25, 2022, at 13:06, Rihab Bayoudhi <bayoudhirihab(a)gmail.com> wrote:        External Email - Use Caution          External Email - Use CautionHi guys! I have followed the virtual machine setup for virtual box freesurfer installation but it ask me the password for the developer account.Which is the password? Cheers, Rihab

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Re: [Freesurfer] Using mri_transform with output of bbregister
by Glasser, Matt 25 Feb '22

25 Feb '22

External Email - Use Caution If you are using high resolution T1w and T2w images with FreeSurfer, you might just run the HCP Pipelines that depend upon such data and take care of all of this. Alternatively, you can see how FreeSurfer is called by the HCP Pipelines: https://secure-web.cisco.com/1FyxUyuquU_ZJL3F2C8HzsVJtR4TjyEcfI1ujxzxMdtGJ9… Lines 680 to 724 Matt. On 2/25/22, 11:23 AM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Tisdall, Dylan" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of mtisdall(a)pennmedicine.upenn.edu> wrote: External Email - Use Caution Hi all, Thanks again for all the help so far with getting my data registered and surfaces extracted. I have one further issue that I'm hoping to get help with. I've used bbregister to align my T2 scan with the surfaces from my T1 scan. However, the output is resampled down to 1mm iso and a 256^3 volume; I'd like to keep the native 0.8 mm resolution and FOV if possible (acknowledging, of course, there's actually some blurring in the interpolation, but just for the sake of nominal consistency). I tried to work around this by applying the .lta output by bbregister to my T2 scan (with the goal of eventually using the --out-like flag to specify the sampling resolution, but not doing that yet): mri_transform T2_SPACE.nii.gz T2_SPACE_transform.lta T2_SPACE_warped.nii.gz However, when I load the resulting output volume (T2_SPACE_warped.nii.gz) in freeview, it has swapped axes. Strangely, this isn't the case with the output volume generated by bbregister... it's well-aligned with the surfaces. Similarly, if I load the T2_SPACE.nii.gz into freeview, and apply T2_SPACE_transform.lta as part of the load command, the volume is well-aligned. So what's different about how mri_transform applies that .lta file, compared to bbregister and freeview? Is there a way to just get bbregister to resample my T2 scan with the original resolution and FOV, so I can avoid applying mri_transform altogether? I don't see an --out-like option for bbregister, but is there a different flag? Thanks again, Dylan _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1K0jT8F3wzx3DuyP8tkCSbM_-KsjwUt_P58Uoc1Km7ywju… ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] Ventricle segmentation issue - ventricle mislabeled as white matter
by Kang, Jee Won 25 Feb '22

25 Feb '22

External Email - Use Caution Hello all, Apologies for the delay in response! For the applications in my group's work, we are looking at ventricular volume, as well as white matter volume. To that degree, we are interested in whether there are any processing steps earlier in the pipeline that we can implement just to minimize the manual editing required - just anecdotally, there have been cases where lateral ventricle volume increases over 5% after making manual edits, and I was unable to identify if there was a common element to the subjects with ventricle problems. Thank you for your work on this! We really appreciate it. Thank you, Jee Won ________________________________________ Message: 2 Date: Tue, 4 Jan 2022 22:11:53 +0000 From: "Nadar, Priyanka (NIH/CC/OCRTME) [F]" <priyanka.nadar(a)nih.gov> Subject: Re: [Freesurfer] [EXTERNAL] Re: Ventricle segmentation issue - ventricle mislabeled as white matter To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <MN2PR09MB5210A46F62E837624F830D51844A9(a)MN2PR09MB5210.namprd09.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" External Email - Use Caution I am not part of Jee Won's team: just generally interested. For my work, I am looking at ventricular volume and so it would be good to not have to manually correct a large number of my scans. ________________________________ From: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Sent: Tuesday, January 4, 2022 1:19 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] Ventricle segmentation issue - ventricle mislabeled as white matter CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe. Hi Jee Won and Priyanka, there are several things going on here. First, the original aseg (aseg.presurf.mgz) has these areas labeled as nothing (0); they show up as WM in aseg.mgz and aparc+aseg.mgz. Obviously, it would be good to have them properly labeled, but is this critical to your applications? Eg, are you looking at ventricular volume? On 12/21/2021 9:19 AM, Kang, Jee Won wrote: External Email - Use Caution Hello all, I found a very common error in our data while I was correcting recons. The lateral ventricles (usually the horns) are being misclassified as white matter in aseg.mgz. This happened in around 1/3 of our 108 subjects. We were able to fix this issue by manually filling in the ventricles in aseg.presurf.mgz and re-running Freesurfer with the command autorecon2-noaseg -autorecon3, but this is obviously quite a labor-intensive fix for a substantial portion of our data. This was also the only way to fix the segmentation - filling in the mislabeled areas as 255 in the wm.mgz did not fix the problem. I'm not sure why Freesurfer is having issues here, as the areas it is mislabeling have very distinct intensity boundaries - the T1 intensity is usually between 20 and 45 in the areas that are being mislabeled. I've attached a screenshot of a subject's aseg.presurf.mgz who had this ventricle segmentation issue, and you can see that a large portion of the right ventricle has just not been segmented properly; the intensity of the area in the aseg.presurf.mgz and wm.mgz volumes is just 0, and it was 41 (R cerebral white matter) in aseg.mgz. Would you be able to provide some insight into why this might have been happening, and what we could do in the future to prevent such extensive manual editing in the future? I can also say that this data was processed with a T2 image as well, and supplying that flag didn't help with the segmentation issue. Thank you, Jee Won _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1ZGRySYd-5iOMX55uEC_0An1dt-wqdEh2tYIkVApSE6ZYz…

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how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics
by Brown, Alexander 24 Feb '22

24 Feb '22

External Email - Use Caution Hello, I have been asked to provide tissue composition stats (%GM,%WM,%CSF) for an SVS VOI. How can I register the svs file to the Freesurfer-processed brain and extract these values? Thanks, Alex Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779

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mri_glmfit of surface CBF maps while regressing out cortical thickness
by Dhungana, Asim 24 Feb '22

24 Feb '22

Dear Freesurfer experts, I am trying to run a GLM analysis comparing the difference in the cortical CBF maps between two groups, but I would like to regress out cortical thickness. I read through a post with a similar question (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65059.html) but I am still a little confused and want to confirm the steps of my analysis below: --- 1. Compile/smooth CBF data on surface for all subjects. mris_preproc --hemi lh \ --projfrac 0.5 \ --target fsaverage \ --o lh.cbf.00.mgh \ --iv subj1/cbf.mgz subj1/register_pasl.dat \ --iv subj2/cbf.mgz subj2/register_pasl.dat \ ... until subjN mri_surf2surf \ --hemi lh \ --s fsaverage \ --sval lh.cbf.00.mgh \ --fwhm 10 \ --cortex \ --tval lh.cbf.fwhm10.mgh 2. Compile/smooth thickness data on surface for all subjects. mris_preproc \ --fsgd cbf.fsgd \ --target fsaverage \ --hemi lh \ --meas thickness \ --out lh.thickness.00.mgh mri_surf2surf \ --hemi lh \ --s fsaverage \ --sval lh.thickness.00.mgh \ --fwhm 10 \ --cortex \ --tval lh.thickness.fwhm10.mgh 3. GLM fit of CBF maps, including thickness as a regressor. mri_glmfit \ --y lh.cbf.fwhm10.mgh \ --fsgd cbf.fsgd \ --pvr lh.thickness.fwhm10.mgh \ --C contrast.ctx \ # where contrast.ctx = "1 -1 0" --surf fsaverage lh \ --cortex \ --glmdir lh.cbf.fwhm10.glmdir \ --eres-save 4. Multiple comparisons correction mri_glmfit-sim \ --glmdir lh.cbf.fwhm10.glmdir \ --perm 1000 1.3 abs \ --cwp 0.05 \ --2spaces \ --bg 35 --- I am currently having issues with Step 4; it has been over an hour, and it seems that the command will not finish executing. It is also not outputting any error messages. Whenever I run this analysis using the same parameters but without regressing out thickness, this step takes under five minutes on my machine and returns appropriate results. It seems like I must be doing something wrong, but I'm not sure. Please let me know if there is anything that you would change/add above. Also, I noticed that you recommended regressing out the overall mean thickness (which you can obtain through mri_glmfit --surf fsaverage lh --osgm --y lh.thickness.fwhm10.mgh --o glm.osgm.lh --eres-save). Is glm.osgm.lh the mean stratified by class or the overall mean? If I were to include this in my GLM fit, would this be the correct command: mri_glmfit \ --y lh.cbf.fwhm10.mgh \ --fsgd cbf.fsgd \ --pvr lh.thickness.fwhm10.mgh glm.osgm.lh \ --C contrast.ctx \ # where contrast.ctx = "1 -1 0 0" --surf fsaverage lh \ --cortex \ --glmdir lh.cbf.fwhm10.glmdir \ --eres-save Thank you for taking a look at this, let me know if you need any other information. Best, Asim Dhungana Freesurfer version: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b

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