Freesurfer October 2023

freesurfer@nmr.mgh.harvard.edu

69 participants
95 discussions

Advice for measuring cortical thickness from a custom label
by Tyler J Ward 02 Nov '23

02 Nov '23

External Email - Use Caution Hi FreeSurfer developers and community, I have a template space statistical surface map that I want to extract cortical thickness and volume from several thousand MRIs with freesurfer parcellations. I converted the map to a cortical label using *mri_surfcluster.* > *mri_surfcluster --in sig.mgh --thmin 4 --sign neg --hemi lh --subject > fsaverage --olab ./my_label --cortex* > [image: unnamed.png][image: unnamed2.png] I then converted these template space labels to subject space labels using mri_label2label. > *mri_label2label --srcsubject fsaverage --srclabel ./**my_label**.label > --trgsubject bert --trglabel ./**burts_label* > *.label --regmethod surface --hemi lh* > Lastly I extracted thickness and created volumes from these labels. > *mri_segstats --slabel bert lh **burts_label* > > *.label --i $SUBJECTS_DIR/bert/surf/lh.thickness --nonempty --excludeid 0 > --sum ./bert_thickness_table**mri_label2vol --o ./berts_mask.mgh --label > ./**berts_label**.label --temp $SUBJECTS_DIR/bert/mri/nu.mgz --subject > bert --hemi lh --fillthresh 0.3 --proj frac 0 1 .1 --identity* > The results look okay but the voxels are not as clean as other freesurfer volumes and ROIs. For example, the cortical masks created from the label have small holes inside the mask. [image: 2023-10-06T16:24:00,146947999-07:00.png] I decided to smooth this by 3mm^3 fwhm and threshold by the left hemisphere cortical parcellation in aparc+aseg.mgz file to get a better looking ROI that is contained by and filled into the freesurfer cortical parcellation: [image: 2023-10-06T16:23:51,051653286-07:00.png] [image: 2023-10-06T16:37:34,665543751-07:00.png] From this, I have a couple questions: 1.) Can I expect my custom ROI thickness to be comparable to the thickness values outputted by Freesurfer for the Deikan-Killiany atlas? 2.) Is there anything I can do to verify the accuracy of the cortical thickness within this ROI? 3.) How can I extract volume from this ROI (should I just count voxels?) and will it be valid to do a cross-sectional analysis of volume from a region derived from a surface label, just as we look at any other region (tiv adjusted hippocampal volume for example)? Thanks in advance for your time and advice, Tyler

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registration of a rescaled volume
by Malav Shah 02 Nov '23

02 Nov '23

External Email - Use Caution Hi there, I have an animal brain's MRI with 3 volumes, each with a good resolution in one of the planes. (i. 768x768x88, ii. 768x768x150, iii. 768x768x140) As far as I understand freeSurfere doesn't have a 3D ihgh-res reconstruction tool, right? So I tried to reconstruct a high-resolution 3D volume with NiftyMIC ( [ https://secure-web.cisco.com/1pycZ_2SF5XqnaigDfeUBVSUx6el0NqrRFY73S86xcHKBm… | https://secure-web.cisco.com/1pycZ_2SF5XqnaigDfeUBVSUx6el0NqrRFY73S86xcHKBm… ] ), but unfortunately it didn't work for me. My final goal is to get good tissue segmentation (pial-, grey-, and white-matter labels). So now I am considering rescaling one of the scans in a high-dim. space (768x768x768) using imresize3 (or something similar for interpolation) with MATLAB. The rescaling works, but the non-high-resolution planes turn out to be elongated. I am not sure how to get past this issue, and register the new rescale volume with one of the old ones (trying some params with mri_vol2vol might work?) At the end I want to visualize rescaled 3D volume on top of the original scans, so I can at least (semi-automatically and then) manually segment it. thanks in advance :) - malav Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. (+49) 163-216-9391

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ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) on fMRIprep
by Siegel-Ramsay, Jennifer 02 Nov '23

02 Nov '23

External Email - Use Caution Hello, We are trying to run freesurfer through fMRIprep and for the first time ever, I have a series of anatomical scans that are failing during registration. Normally we run this on the normalized T1 scan outputs and have no problem, but these are the original images non-normalized images. My random guess is that there might be too much inhomogeneity in the T1 signal to run freesurfer? I am very new and have rarely used freesurfer. Here is the fMRIprep error (full log attached) #@# Talairach Failure Detection Mon Oct 2 15:32:02 CDT 2023 /work/06950/j/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See: http://secure-web.cisco.com/1kkJIUzEvH0ScGRNqsTstzKtzyE2xMeizp0oaQP3-n-ioGW… Ok, I've tried going through this https://secure-web.cisco.com/1QtKKJUk_dNKuv9HQvIxbFlVKsOnN9ROC0VGd25vitNurR… to figure out what is going wrong with the T1 images during the freesurfer registration with fMRIprep. Freesurfer isn't liking our T1 images. This image is the freesurfer output (output under derivatives/frmiprep/sourcedata/sub-ut0002/mri/T1.mgz [cid:image005.png@01D9F782.EC5FF0E0] The above should come out registered to this one which is the sub-ut0002/mri/brainmask.mgz:reg=sub-ut0002/mri/transforms/talairach.xfm [cid:image006.png@01D9F782.EC5FF0E0] I can't go in and manually alter the T1 to be in alignment in tkregisterfv because I don't have any of the needed files output in the surf folder. Getting... ERROR: cannot find /home/jovyan/freesurfer-subjects-dir/sub_ut0002/surf/lh.white I am attaching the full crash log from fMRIprep and also the script output. I wonder if you could help me understand what might be going wrong? Thanks, Jennifer Jennifer Siegel-Ramsay, PhD Postdoctoral Fellow Department of Psychiatry and Behavioral Sciences Dell Medical School | The University of Texas at Austin dellmedschool.utexas.edu<../../../../../lep66/AppData/Local/Microsoft/Windows/INetCache/Content.Outlook/H3ICGTO9/dellmedschool.utexas.edu>

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Project volumetric MTR data on surface
by Davide Tabarelli 02 Nov '23

02 Nov '23

External Email - Use Caution Dea FreeSurfer experts, I’m writing in order to ask how to map on a surface data from a volumetric MTR image. I have volumetric Magnetization Transfer Ratio data co-registered to the subject native space of a subject (as produced by recon-all on a T1 acquisition). The subject, for which I have also the T1 and T2 scans, has been already processed with recon-all, then I have the complete folder of the subject, as produced by the recon-all standard pipeline. I need a surface in the native subject space containing the MTR data, averaged along the surface normals for a certain amount of millimeters. It would also be useful to define the surface as in a certain midway between the pial and the white surfaces. I tried to understand the mri_vol2surf tool but I’m stuck in understanding the correct way to do this and if this is the correct command to be used. I would greatly appreciate your help ! Thank you in advance. Davide

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Possible Skull-Stripping Error in Many Subjects (FS7.2)
by Carly McIntyre-Wood 02 Nov '23

02 Nov '23

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FSGD file and constrast
by Steve Petersen 02 Nov '23

02 Nov '23

External Email - Use Caution Dear FreeSurfer experts, I have MRI data of one group of subjects and would like to evaluate positive and negative correlations between cortical thickness and some biomarkers by excluding the potential effects of age and sex. I followed the FS tutorials ( https://secure-web.cisco.com/1Y5TdIEJ9ARZSn2I1-6PLi22V0MhAKTkmre4K1MKlAmgQh…) and have read previous posts on the FS´s mail archive but I would appreciate if you can check if my FSGD file and contrasts are right. The FSGD file looks as follows: GroupDescriptorFile 1 Title CTh_Bioma Class Female Class Male Variables age biomarker Input 4009 Female 60 222.0 Input 4014 Male 70 195.6 Input 4022 Male 68 230.2 Input 4027 Female 65 250.0 Input 4039 Male 62 205.6 Input 4001 Male 63 270.2 Input 4002 Male 78 245.5 Input 4004 Male 66 234.1 Input 4050 Female 62 210.0 And these would be my contrasts: positive correlation between thickness and the biomarker: 0 0 0 1 negative correlation between thickness and the biomarker: 0 0 0 -1 Thank you very much in advance. Best regards, Steve.

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[FreeSurfer] regeneration of aseg.stats from manually edited aseg.mgz
by Krystal Xiwing Yau 02 Nov '23

02 Nov '23

External Email - Use Caution Dear FreeSurfer experts, I edited some images that under-segmented the brain by coloring the missing brain regions. When I used the edited aseg.mgz to regenerate aseg.stats, the new statistics did not show the increase of the volumes that I edited. Please see the following command lines that I have run on Linux: mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject Sub-180 May I know what step(s) I have missed before generating the aseg.stats? Please kindly advise. Thank you very much! Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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Tkregister2 GUI not responding fully
by Viktorija Pratuseviciute 02 Nov '23

02 Nov '23

External Email - Use Caution Hello, We are trying to process a scan with a failed talairach. We have been able to visualize the misalignment and attempted to use the following command (tkregister2 --s PI163 –fstal) to manual adjust the talairach.xfm based on the tutorial (https://secure-web.cisco.com/1acx6rTd53-Vz7knc_wTrpqifC8PTuiKKanQydzd8QVOyX…) The tkregister2 GUI opens up, however only certain functions work: I can switch between target and moveable, I can also double click on sliding scales to switch coronal, saggital and horizontal views, however I am not able to move any of the sliders including the rotate or translate brain and hence unable to fix the talairach. Is there a way to fix this issue? Or an alternative way to fix the bad talairach output? We are using freesurfer/7.3.1 and have attempted the command on our server command line on both mac and windows with same results. Many thanks, Viki

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Re: [Freesurfer] Slow processing of large defect
by fsbuild 02 Nov '23

02 Nov '23

External Email - Use Caution  If your host machine has 32G of RAM, then it should work to give the VM 16G or perhaps even 24G of RAM. If most all swap space is in use, then it’s likely something is under-running or exhausting the available physical RAM.   Some machines start to swap what’s in memory out to disk files when only 80% of RAM is in use.  But disk I/O from loading swap files in/out of memory can cause the machine to slow down or thrash and never finish processing.  With no consequential or RAM hungry applications running on the host, then the host should be able to essentially run idle with 8G of RAM leaving 24G to assign to the VM. - R. On Oct 3, 2023, at 02:01, Pål Gunnar Larsson <pall(a)ous-hf.no> wrote:        External Email - Use Caution        Thank you for fast reply..The computer has 32Gb. The virtual machine has 8Gb. According to ‘top’ all is used, except 140Mb. Swap has 1Gb of which 780Mb is used. Does swapping use lots of CPU? It is 100% most of the time. Fra: fsbuild <fsbuild@contbay.com> Sendt: 3. oktober 2023 04:33Til: freesurfer@nmr.mgh.harvard.eduKopi: Pål Gunnar Larsson <pall@ous-hf.no>Emne: Re: [Freesurfer] Slow processing of large defect  Not clear if "8G of RAM" below means 8G is assigned to the VM, or the host machine has 8G RAM total.   Assuming the VM has ~8G assigned then the host should have 16-24G RAM total.It reads like the VM is thrashing, e.g., swapping out to disk due to lack of RAM - which can cause a crash.   I would try running the VM on a host machine that can provide more RAM.  So if the VM is currently running with 8G, then try doubling it to 16G (on a host with at least 24 or 32G RAM).- R.On 10/2/23 10:31, Pål Gunnar Larsson (pall(a)ous-hf.no) wrote:        External Email - Use Caution        Hello I am running FS 7.4.1 on Ubuntu 22.10 on Virtualbox 21.10, having 8Gb of ram. I am running a child-MRI where I got a message about a large defect which would run slowly or crash. FS is still running after more than 10 days (70%-100% CPU use), but there are nothing written to disk for 10 days. It is working on retesselation of defect 162.Is there any reason to wait it out? Or will the results be unpredictable? Best Pål G. Larsson Ikke sensitiv _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1aeEAtzSDgvMg67gOnpL-fUlNHOFDsR1OYOQuJbl5mIkHQ… note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.  _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs
by Huang, Yujing 31 Oct '23

31 Oct '23

It looks like seg2recon is also looking for FREESURFER. Set it to your Freesurfer install directory, same as FREESURFER_HOME. From: Maya Yablonski <mayay(a)stanford.edu> Sent: Tuesday, October 31, 2023 7:08 PM To: Huang, Yujing <YHUANG43(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs External Email - Use Caution Thanks! That seems to do the trick and it started running, but crashed after a few minutes. The log file shows the last thing that ran was this command: seg2recon --s sub-xx --seg PATH/sub-xx/mri/synthseg.rca.mgz --i /PATH/sub-xx/mri/orig.mgz --threads 1 followed by this error: FREESURFER: Undefined variable. Should I define this variable in addition to FREESURFER_HOME and SUBJECTS_DIR? Where should it point to? Thanks for the help! Maya

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Freesurfer October 2023