Freesurfer April 2023

freesurfer@nmr.mgh.harvard.edu

80 participants
105 discussions

Neuroimaging research technician positions available at Washington University in St. Louis
by Keefe, Sarah 13 Apr '23

13 Apr '23

External Email - Use Caution Hi all, The laboratory of Dr. Tammie Benzinger at Washington University in St. Louis is currently hiring for multiple full-time research technician positions in a neuroimaging lab focused on aging and Alzheimer disease. The research technician role is an integral part of the neuroimaging research process. This position focuses on processing of MRI and PET images, including quality control and editing of output from the FreeSurfer MRI image processing software. Technicians also perform other support tasks assisting researchers with their projects, such as organizing large datasets for analysis, tracking project progress, and exploring new image processing methods. No prior knowledge of neuroimaging is required for this position. Technicians will learn on the job and gain technical experience in a research environment. More details on the position and information on how to apply are in the link below. https://secure-web.cisco.com/1eHpeCxb5I7Ji6q1AfVTELFFrM2gJ2tzyjLATJEHOy6adF… Please feel free to forward this message to anyone who may be interested. Thank you! ________________________________ 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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Regarding the Use of Custom atlases containing deep brain nuclei in recon-all segmentation
by Abhishek Prabhu 12 Apr '23

12 Apr '23

External Email - Use Caution Dear Freesurfers, I am a neuroscience master's student and new to free surfer. I had a task of segmenting deep brain nuclei from T1 scans using free surfer, which I was able to do successfully, but ran into some problems. The atlas used by Freesurfer for the segmentation is the Taiairach atlas, which doesn't contain the "Subthalamic nucleus" which is an ROI that I require. Hence I went thoroughly through the mailing list/ free surfer documentation about how I can implement a custom atlas containing subcortical structures ( that is *in.nii format* and has a *CSV file* for the regions in the atlas) in the recon-all function, but I wasn't able to gather any concrete information about how to do so. Hence, I have a kind request as to whether someone can spare me a bit of their precious time and send me a step-by-step guide from their experience with the same problem. Thank you for your time! :) , Warm regards Abhishek

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Re: [Freesurfer] mris_flatten Version 6 vs. 7
by Fischl, Bruce R.,PHD 11 Apr '23

11 Apr '23

External Email - Use Caution Moving the thread back to the list as I don’t know, but maybe someone else does? From: Nasr, Shahin,Ph.D. <shahin.nasr(a)MGH.HARVARD.EDU> Sent: Saturday, April 8, 2023 4:10 PM To: Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu> Subject: Re: mris_flatten Version 6 vs. 7 it doesn't exist in the cut, and I do not see it in the outcome of version 6 (attached). Shahin Nasr, Ph. D. Assistant Professor in Radiology Harvard Medical School https://secure-web.cisco.com/11YPf2MPvXvH0nit4jHDe36YSTq-NvOFFUASunejUkkR9F… ________________________________ From: Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Sent: Saturday, April 8, 2023 12:02 PM To: Nasr, Shahin,Ph.D. <shahin.nasr(a)MGH.HARVARD.EDU<mailto:shahin.nasr@MGH.HARVARD.EDU>> Subject: RE: mris_flatten Version 6 vs. 7 Oh, looks like you had a small cut there From: Nasr, Shahin,Ph.D. <shahin.nasr(a)MGH.HARVARD.EDU<mailto:shahin.nasr@MGH.HARVARD.EDU>> Sent: Saturday, April 8, 2023 12:02 PM To: Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Subject: Re: mris_flatten Version 6 vs. 7 In the attached file, I zoomed in and enlarged the location so you can see the issue. Regards Shahin Nasr, Ph. D. Assistant Professor in Radiology Harvard Medical School https://secure-web.cisco.com/11YPf2MPvXvH0nit4jHDe36YSTq-NvOFFUASunejUkkR9F… ________________________________ From: Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Sent: Saturday, April 8, 2023 11:54 AM To: Nasr, Shahin,Ph.D. <shahin.nasr(a)MGH.HARVARD.EDU<mailto:shahin.nasr@MGH.HARVARD.EDU>>; Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: RE: mris_flatten Version 6 vs. 7 Sorry, I don’t see what black dot you are referring to. As for being different, when the distances it uses are random it will change run to run. Basically you hope some of them prevent the patch from folding on itself (which it will definitely be prone to if the distances are only nearest neighbor) From: Nasr, Shahin,Ph.D. <shahin.nasr(a)MGH.HARVARD.EDU<mailto:shahin.nasr@MGH.HARVARD.EDU>> Sent: Saturday, April 8, 2023 11:47 AM To: Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>>; Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: mris_flatten Version 6 vs. 7 Hi Bruce, Adding -distance 20 20 definitely helped (see the attached file). Even though, the outcome is still different than what we see based on Version 6 (my previous emails), which might be OK. But do you notice the black dot (missing vertex) at the tip of calcarine sulcus? Any idea why that is happening? Any solution for that? Regards, Shahin Nasr, Ph. D. Assistant Professor in Radiology Harvard Medical School https://secure-web.cisco.com/11YPf2MPvXvH0nit4jHDe36YSTq-NvOFFUASunejUkkR9F… ________________________________ From: Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Sent: Saturday, April 8, 2023 10:14 AM To: Nasr, Shahin,Ph.D. <shahin.nasr(a)MGH.HARVARD.EDU<mailto:shahin.nasr@MGH.HARVARD.EDU>>; Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: RE: mris_flatten Version 6 vs. 7 Can you try running it with -distances 20 20 added to the command line? From: Nasr, Shahin,Ph.D. <shahin.nasr(a)MGH.HARVARD.EDU<mailto:shahin.nasr@MGH.HARVARD.EDU>> Sent: Saturday, April 8, 2023 8:59 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Cc: Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Subject: Re: mris_flatten Version 6 vs. 7 Dear Bruce, I ran mris_flatten with -norand flag (mris_flatten -norand rh.occip.patch.3d rh.occip.patch.flat) and it still fails (see the attached file). I can share the patch with you if you want. But it is a surprise because version 6 generate the flattened patch without any problem. Also FYI, this problem is NOT limited to this specific patch. I have applied it to multiple other occipital patches (from other subjects) and the outcome is the same. Regards, Shahin Nasr, Ph. D. Assistant Professor in Radiology Harvard Medical School https://secure-web.cisco.com/11YPf2MPvXvH0nit4jHDe36YSTq-NvOFFUASunejUkkR9F… ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Sent: Friday, April 7, 2023 5:21 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7 Yes, well, that is totally my fault! Doug is much better about adding help text than I am ☹ Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Nasr, Shahin,Ph.D. Sent: Friday, April 7, 2023 5:18 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7 Hi Bruce, In both versions, I use this command: mris_flatten rh.occip.patch.3d rh.occip.patch.flat They are applied to the same patch. Also may be I missed it but when I used help (mris_flatten --help) I didn't see any of these flags. Regards, ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Sent: Friday, April 7, 2023 5:11:49 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7 External Email - Use Caution Hi Shahin What is your command line? mris_flatten does some random sampling of distances since the whole N^2 distance matrix is too big. You can remove the randomness by either specifying -norand or using a specific seed like -seed 1234. That said, you second image looks like a failure of the flattening. This usually means the distances aren’t sampled out far enough/densely enough. The defaults are super old (7 neighbor ring, 12 distances/ring). You could try something like -distances 20 20 and see if that fixes things (and -norand if you want) Cheers Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Nasr, Shahin,Ph.D. Sent: Friday, April 7, 2023 3:15 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] mris_flatten Version 6 vs. 7 External Email - Use Caution Hi Surfers, This is the second time that I have brought this issue up. When applied to the same 3D patch, the command mris_flatten generates two completely different outcomes when runs under stable 6 vs. 711 (see the attached files). I checked the documentation if there is any flags by which I can control the process. But I couldn't find anything relevant. Any idea what has happened? Regards Shahin Nasr, Ph. D. Assistant Professor in Radiology Harvard Medical School MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/11YPf2MPvXvH0nit4jHDe36YSTq-NvOFFUASunejUkkR9F…<https://secure-web.cisco.com/1KKZlmmfbSaMq_e7vZdb7bVOx0Po2Sy-YscOPY5REFynzc…>

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Concerns About Acquisition Parameters Biasing Longitudinal Study Results
by NicolasNorton 11 Apr '23

11 Apr '23

External Email - Use Caution Dear Freesurfers, I hope this email finds you well. I am writing to you because I have concerns about how acquisition parameters are biasing the results of a longitudinal study I am running on Niftis that I have processed with Synth_SR. Specifically, when I run the -base command, I receive a message indicating that the scan parameters do not match and that this may bias the results. As a test, I compared longitudinal MRIs for one subject using both T1 and FLAIR scans. I then used the long_mris_slopes function on both pairs and compared the resulting long.volume-pc1.FWHM10.fsaverage.mgh files. Surprisingly, I found that the areas of significance were different between the two scans. This suggests that the acquisition parameters used in the scans are biasing the results of my longitudinal study. I am therefore seeking advice on how to correct for this issue. Do you have any recommendations or best practices for ensuring that acquisition parameters do not bias longitudinal study results? Any advice or guidance you can provide would be greatly appreciated. Thank you for your time and consideration. I look forward to hearing back from you soon. Best regards, Nicolas

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Paired analysis contrast with multiple classes
by Christoph Aster 11 Apr '23

11 Apr '23

External Email - Use Caution Dear Freesurfer Team, I have a dataset with 50 subjects and two timepoints. I would like to see the effect of TP1-TP2, corrected for the covariates age, sex, scanner. I have run the paired_diff analysis with my longitudinal processed data. My second fsgd file now likes this: GroupDescriptorFile 1 Title Pre_Post_KM_with_sex_age_scanner_as_CV Class 0_1 Class 0_2 Class 0_3 Class 1_1 Class 1_2 Class 1_3 Variables age 002pair 0_2 18 004pair 0_3 19 005pair 0_1 19 008pair 0_0 21 010pair 0_2 23 012pair 1_1 24 013pair 0_2 24 015pair 1_2 27 016pair 1_1 27 018pair 1_1 28 019pair 0_2 28 022pair 1_1 32 023pair 0_1 32 024pair 0_3 33 0_1 means female sex on scanner 1. 1_2 means male sex on scanner 3 and so on... So this means I have 6 intercepts and 6 slopes, and my contrast file has 12 inputs. If I just want the effect between timepoint 1 and timepoint 2, controlling for class and age, how should my contrast file look like? If I use 1.6 1.6 1.6 1.6 1.6 1.6 0 0 0 0 0 0 I get no significant clusters which is unlikely when I compare the tabulary data (aseg2stats e.g.) My command for mri_glmfit was: mri_glmfit --glmdir lh.paired-diff --y mgh_files/lh.paired-diff.volume.mgh --fsgd paired_diff_with_CV.fsgd --C mean_with_cv.mtx --surface fsaverage lh --nii.gz To display the results it was: tksurferfv fsaverage lh inflated -aparc -overlay /data/Aster_H/Daten/Freesurfer_Longitudinal/Schreglman_S/fsgd/lh.paired-diff/mean_with_cv/sig.nii.gz -fminmax 2 3 Thank you for your help an kind regards Hans

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T1 with contrast
by Carlos Alcocer 11 Apr '23

11 Apr '23

External Email - Use Caution Can you use T1 with contrast in freesurfer or does it have to be non-contrast images? Tks, Carlos

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Subcallosal cingulate cortex segmentation/parcellation
by Carlos Alcocer 11 Apr '23

11 Apr '23

External Email - Use Caution Hi, I am interested in the aparc+aseg stats for the subcallosal cinuglate cortex (SCC). When learning freesurfer, the lectures/tutorials mention not to make manual edits to medial structures which I believe would include the SCC. Will the stat output files still be accurate if I don't make edits to these areas given that the surfaces can look quite messy in those areas at times? Thank you, Carlos

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dcmunpack behavior with scouts
by Proulx, Jean Sebastien 11 Apr '23

11 Apr '23

Dear Freesurfer Team, The help of dcmunpack says it will ignore scout scans. Is there perhaps a hidden flag to avoid that behavior? We are running multiple scouts throughout a session to combat head motion. Getting those images along the rest would allow visualizing that motion offline. Thanks for your attention and Have a very good day! Sébastiem

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Zip File Passcode
by Mike Iatrakis 10 Apr '23

10 Apr '23

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How to create a functional ROI on surface where activation is peak?
by Andy Kim 09 Apr '23

09 Apr '23

External Email - Use Caution Dear FreeSurfer developers, Hi. I've always appreciated your help. I am writing this email to kindly ask you how to create a functional ROI where activation (which is a result of FS-FAST) is peak. In volume-based analysis, people often make a "3mm-sphere" seed around peak activation for connectivity analysis. But since it is surface based, there is no "3mm-sphere". Then what would it be for surface? I tried: mri_surfcluster --in ./masked_sig1.nii.gz --hemi lh --subject fsaverage --thmin 5 --sum ./summary1.txt, but its output is not actually what I want. It tells peak X, Y, Z coordinates, but I want a fixed size of small cluster (like 3mm-sphere in volume) for creating a ROI in different masks (like peak ROI in V1, peak ROI in V2, etc). In addition, minimum threshold may be diffrent depending on masks. By this I mean, if I choose thmin of 5 for both V1 and V2, V1 may have a huge cluster where vertices have values greater than 5, where as V2 may have a small cluster. I just want to get a fixed size of ROI around "peak". How should I make a functional ROI around peak activation on surface? Kind Regards, Andy (Junghyun) Kim

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Freesurfer April 2023