Freesurfer November 2022

freesurfer@nmr.mgh.harvard.edu

80 participants
119 discussions

Pass code for archive "FS_7_2_0_Ubuntu_18_04_06.ova.7z"
by Диляра Айнуллова 20 Nov '22

20 Nov '22

External Email - Use Caution Hello! My name is Dilyara. I’m student of Kazan State Medical University and I’d like to use your programm for my science work. At this guide https://secure-web.cisco.com/1GwjFRQ-2FvgOFd6Y8S6_UDcGBJRfOPG2YVvMfZxJnTB3r… I saw lines "If you do not have the pass code to open the image, then send an email to the FreeSurfer help list to receive it." May I ask you to send me pass code for archive "FS_7_2_0_Ubuntu_18_04_06.ova.7z" -- Dilyara Aynullova Отправлено из Почты Mail.ru

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FS 7.2 Ubuntu pass required
by Tabasi, Farhad 18 Nov '22

18 Nov '22

External Email - Use Caution Hello, I am installing the Virtual Machine to run Freesurfer, and I prompted with a password. Could you please share the password with me? Thank you for your help. Regards, Farhad Tabasi

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Supplying a mask to recon-all?
by Xinyu Liu 18 Nov '22

18 Nov '22

External Email - Use Caution Dear experts, I am trying to use freesurfer with a set of high-resolution images (0.6mm3 isotropic) and I found the brain mask generated by freesurfer is not ideal. In this case, is it possible to supply a mask to recon-all? I've seen in previous communications it has been suggested to run auto-recon1, replace the mask and proceed with auto-recon2 etc, but I was hoping to use recon-all directly if that's possible. Or is it possible to run recon-all with skull-stripped image? Thank you very much. Best Xinyu

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Passcode request
by emma.sophie＠gmx.net 18 Nov '22

18 Nov '22

External Email - Use Caution Dear Sir or Madam, I would like to request the passcode for the FS_7_2_0_ubuntu_18_04_06.ova.7z file. I can`t open it without one. Thank you very much for your help. Yours sincerely, Emma Wiedenmann

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Fwd: Longitudinal FS pipeline consistently interrupts at -Sphere for all participants
by Julie Ottoy 17 Nov '22

17 Nov '22

External Email - Use Caution Hi FS team, Just wanted to follow up with my question below. Thanks! Julie ---------- Forwarded message --------- From: Julie Ottoy <julie.jj.ottoy(a)gmail.com> Date: Fri, 4 Nov 2022 at 00:11 Subject: Re: [Freesurfer] Longitudinal FS pipeline consistently interrupts at -Sphere for all participants To: fsbuild <fsbuild(a)contbay.com> Hi Fsbuild team, Thank you for your reply. Sorry for the confusion, my system was actually Linux, not Windows. It did *not* run on top of Windows (sorry again for the confusion). In any case, I tried both the longitudinal pipeline FS v7.1.1 and v7.2 consistently on Linux. I also used two different machines (our institute server as well as ComputeCanada, hence I do not believe it's a memory issue). Each run got stuck at the -Sphere x.long.x step as indicated in my previous email. Interestingly, I tried today with the longitudinal FS v6.0.0 (kept all the rest the same) and it ran fine! Could there be any bug in the v7 series for longitudinal processing that was not present in the v6 series? I tried on two different types of input T1w data acquired from different centers and they point to the same issue => -Sphere error in x.long.x for v7 , while it runs fine for v6. Please see attached log files and screenshots for both. I am also thinking if it would be ok to run the longitudinal with v6 since we ran the baseline data with v7.2. Could you please advise on this? Last, I was wondering if there is a way to receive more detailed log/error files? As indicated from my previous email and screenshots, the code just exited at Sphere but did not indicate why it went wrong there. Thank you for your help! Best regards Julie On Wed, 2 Nov 2022 at 17:02, fsbuild <fsbuild(a)contbay.com> wrote: > One way we’ve seen recon-all eventually fail running on Linux hosted on > Windows is whatever is virtualizing Linux to run on top of the Windows OS - > simply runs out of memory at some point in the processing pipeline. That > can result in a message in the recon-all.log like a file was not found, > i.e., a computation fails and the results are not saved in a file that > later on is expected to be found, opened and read. I don’t see messages > like that in your log. > > It might be helpful to know more about how you are running Linux on > windows, e.g., if you are using the built-in Windows Subsystem for Linux > (WSL) or using a VM running on something like VirtualBox. > > You could also send along the output in the linux terminal from: > $ cat /etc/os-release > $ cat $FREESURFER_HOME/build-stamp.txt > > - R. > > On Nov 2, 2022, at 15:03, Julie Ottoy <julie.jj.ottoy(a)gmail.com> wrote: > > <recon-all.log> > > >

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Medial wall mask for FSL tractography
by Renew Andrade 17 Nov '22

17 Nov '22

External Email - Use Caution Dear experts: I have a doubt about finding the medial wall mask of a subject. Would this be ok? mri_label2label --srclabel lh.cortex.label --trglabel lh.cortex.label --outmask lh.cortex.mask.nii.gz --regmethod surface --hemi lh --srcsubject 25633 --trgsubject 25633 fscalc lh.cortex.mask.mgz not -o lh.medialwall.mask.mgz mri_convert lh.medialwall.mask.mgz lh.medialwall.mask.gii If I use mris_decimate to downsample the surface does it change anything of previous and how should I proceed in that case to change it? Best, Rene Andrade.

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Effect size, Plotting and Heat maps
by Lyna Mariam El Haffaf 17 Nov '22

17 Nov '22

External Email - Use Caution Dear Freesurfer team, My colleagues and I performed a general linear model with FreeSurfer mri_glmfit for whole brain analysis in intergroup comparison (g2v1) with a Monte-Carlo correction. I'd like to get the effect size of the analysis and I was wondering how could I get the eta squared or R2? I I also saw that the gamma.mgh file was the contrast effect size. Could this be used as an effect size for this type of analysis? I was also wondering if it was possible to plot the results from the GLM and getting a linear regression with the ROI as the y axis and neuropsychiatric symptom severity on the x axis and displaying both groups (Alzheimer vs Mild cognitive impairment) in one plot? If it is possible, how can I do this? I found a plotting script (https://secure-web.cisco.com/1J2MTZ3C6wunLISy_F5rLCagiGKjtD_DqkJHs5AfuTnjbX…) but it was for FDR corrected, not Monte-Carlo. Finally, I was also wondering how could I display a heat map or gradient shading based on neuropsychiatric symptoms severity on the image from the significant regions I got from the GLM with freeview? Thank you in advance! Lyna El Haffaf Graduate student in neuropsychology University of Montreal

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Mapping the labels onto the aparc atlas
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 17 Nov '22

17 Nov '22

External Email - Use Caution Hi Freesurfer devs, We have used mri_aparc2aseg to map the Stanford mpm/vpnl labels unto the gray matter ribbon. We notice that when analyzing the resulting mpm.vpnl+aseg.mgz that the regions/voxels of the mpm.vpnl+aseg.mgz stretch out the corresponding voxels that the labels identify as the mpm/vpnl. Can we reliably use the mpm.vpnl+aseg.mgz, and are the stats created from that file, or from the annot file? We are asking because we are using the mpm.vpnl+aseg.mgz as a mask for blood perfusion measurements. Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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Recon-all output in MNI305, patient space, or other?
by Andrew M 17 Nov '22

17 Nov '22

External Email - Use Caution Greetings, I am running recon-all as per the iElvis pipeline with: recon-all -s <id> -i $SUBJECTS_DIR/.../T1.nii -all -localGI And followed by ct2mri My questions are: 1. What is the actual output "space" of the resulting T1.nii and postInPre.nii ? Does recon-all do keep everything in patient space, or does it register them to fsaverage space automatically? If so, how would I convert these MRIs and CTs to MNI305 space? Thank you very much. Andrew

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--pv flag in mri_segstats
by Julie Ottoy 17 Nov '22

17 Nov '22

External Email - Use Caution Hello FS team, If I want to calculate the average diffusion-weighted signal from a DWI image within WM regions using mri_segstats, would it be beneficial to use the --pv flag for "partial volume correction" , or would this only have an influence on the Volume calculation? mri_segstats --seg ${whitemattermask} --i ${DTI_image} --sum ${ whitematter_stats} --excludeid 0 or norm=${subject}/mri/norm.mgz mri_segstats --seg ${whitemattermask} --i ${DTI_image} --sum ${ whitematter_stats} --pv ${norm} --excludeid 0 Thanks, Julie

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Freesurfer November 2022