Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

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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Re: [Freesurfer] Annotation File to ROI Volume Estimate
by Jacoby, John 24 Feb '22

24 Feb '22

Hi Doug, thanks for the pointer. That was exactly what I was looking for. When I copied the command from recon-all.log, it used a -b flag. I can't find documentation for this flag either in the --help or on the wiki. Could you elaborate on what it does? Thank you! Best, John

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Dividing surface overlays
by Tisdall, Dylan 24 Feb '22

24 Feb '22

External Email - Use Caution Hi all, I've generated two surface overlays, using mri_vol2surf with positive and negative projfrac to get a GM and WM samples (gm_lh.nii.gz and wm_lh.nii.gz). I'd now like to take the vertex-wise ratio of these two overlays, and make a new one (gmwmratio_lh.nii.gz). I've tried doing this as: fslmaths gm_lh.nii.gz -div wm_lh.nii.gz gmwmratio_lh.nii.gz but the result is: Image Exception: #22 :: Failed to read volume gm_lh.nii.gz Error : Error: Nonsensical ROI for gm_lh.nii.gz Is there another tool I can use to compute this ratio? Is there a better workflow than making two surfaces and dividing? Thanks, Dylan

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SAMSEG "lesion" (Illegal instruction) ~ running VM_67
by daedalus39＠aol.com 24 Feb '22

24 Feb '22

External Email - Use Caution Dear 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 error Illegal 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

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Mass-univariate LME - contrast for one group
by Franziska Haase 24 Feb '22

24 Feb '22

External Email - Use Caution Dear experts, Sorry, for posting again - I was not able to answer on my first post, don't know why. If anyone has an idea about this, please let me know! Unfortunately, I did not make any progress. Best, Franziska External Email - Use Caution Dear FreeSurfer experts, I am trying to use the spatiotemporal mass-univariate LME approach for my data but am struggling with choosing the right contrast. I have one group with 14 subjects, two timepoints for each subject and age. My goal is to test whether the subjects experienced any kind of change in cortical thickness from pre- to post-measurement, controlling for age. I followed the tutorial up to the point where I figured out that only one random effect is needed as most vertices did not survive multiple comparisons correction. If I am correct the next step is to test, whether a quadratic or a linear model is needed. Therefore, I tested the contrast CM1.C = [0 1 0 0] on my design matrix X with subjects, time in years, (time in years)², age: 1.0000 0 0 20.0000 1.0000 1.4800 2.1904 20.0000 1.0000 0 0 19.0000 1.0000 1.4800 2.1904 19.0000 ... Multiple comparisons correction revealed an empty vector (as in the tutorial), so that the quadratic term of time was removed and a linear model with one random effect is tested with the new design matrix 1.0000 0 20.0000 1.0000 1.4800 20.0000 1.0000 0 19.0000 1.0000 1.4800 19.0000 ... Next, I applied the contrast CM2.C=[0 1 0] to test for change over time. My question is if this is actually the right way to achieve my goal or whether I am doing something completely wrong. And if it is correct, I would go on by correcting for multiple comparisons, right? How would I visualize the results & additionally get information about significant clusters? Unfortunately, it seems like I am not understanding the last part of the tutorial. Any help would be much appreciated! Best, Franziska _____________________________ Franziska K. Haase, M.A. Sportmedizinisches Institut Department Sport und Gesundheit Fakultät für Naturwissenschaften Universität Paderborn Warburger Str. 100 33098 Paderborn Golfakademie 20b _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1ZxGOXwI-5I_nFKnzGJh-8sbjYxGtRJOXvHqwmkT48MJ8t…

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Error sending tcl command
by Yuhui LIANG 梁玉慧 24 Feb '22

24 Feb '22

External Email - Use Caution To whom it may concern, How are you recently? I am trying to follow the the ENIGMA Cortical QC protocol to check my external surface result after order "recon-all". The detail of scripts is attached bolow (here<http://secure-web.cisco.com/1dkHKFt2pSHfUZ0kA6gifWjCITDX34GWZl6d7V5zMMqr8bm…>). I used "tksurfer" to get a series of 4 images (.tif) files for each subject. But I always met this type of error. surfer: Error sending tcl command LblLst_UpdateInfo 33 "frontalpole" 32 1 100 0 100: invalid command name "LblLst_UpdateInfo" surfer: Error sending tcl command LabelsChanged: invalid command name "LabelsChanged" When I tried to solve this problem, I noticed that the "freesurfer" was cannot support "tksurfer" any more. In stead, they suggested users to run another command "tksurferfv" , which will run freeview with most of the "tksurfer" command line options. But both of tksurferfv and freeview can not support "tcl" command. The error is written as below. Everytime I trid to run this script, I always found this error. Option 'tcl' not recognized. By the way, I wanna notify you that I am using freesurfer version 7.2.0 in CentOS 8. How can I overcome this problem? Any advice would be appreciated! Sincerely, Yuhui

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