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30132 discussions

Re: [Freesurfer] no register.dat file for mri_label2vol
by Ayzenberg, Vladislav 27 Jul '18

27 Jul '18

External Email - Use Caution Greetings, I am trying to convert a surface label (e.g., lh.V1_exvivo.thresh.label) into a volume to use as an ROI mask. I have played around with the mri_label2vol command, but I can't seem to get it to work. Here is the command I am using: mri_label2vol --label lh.V1_exvivo.thresh.label --temp T1.mgz --reg register.dat --fillthresh .3 --proj frac 0 1 .1 --subject sub1 --hemi lh --o V1Test.nii.gz The issue I believe is that I don't have seem to have a register.dat file. However, I'm not sure how to generate the relevant registration file since the surface label I'm using is already in subject space. The label that I need was created when I used recon-all to generate surfaces from my anatomical image. If it is relevant, my original anatomical image is a skull stripped T1 generated using FSL which I then converted to .mgz. Does anyone have any insight? Thank you! Vlad ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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error during volume_stats
by Russell Butler 27 Jul '18

27 Jul '18

External Email - Use Caution i receive this error when i try to run recon-all from my home directory on neurodebian: anyone know what is causing this? thanks, Iteration 1 Fri Jul 27 09:24:33 EDT 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.2638/nu0.mnc ./tmp.mri_nu_correct.mni.2638/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2638/0/ -iterations 1000 -distance 50 [brain@neurodebian:/home/brain/fstest/test1/mri/] [2018-07-27 09:24:33] running: /opt/minc/1.9.16/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.2638/0/ ./tmp.mri_nu_correct.mni.2638/nu0.mnc ./tmp.mri_nu_correct.mni.2638/nu1.imp /opt/minc/1.9.16/bin/volume_stats: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /opt/minc/1.9.16/bin/volume_stats) nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct Linux neurodebian 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt9-3~deb8u1 (2015-04-24) x86_64 GNU/Linux recon-all -s test1 exited with ERRORS at Fri Jul 27 09:24:33 EDT 2018 For more details, see the log file /home/brain/fstest/test1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Resting-State and Brain Connectivity 2018: Added Events & Submission Deadline (fwd)
by Bruce Fischl 26 Jul '18

26 Jul '18

FYI ---------- Forwarded message ---------- Date: Fri, 27 Jul 2018 01:43:03 +0000 From: "Amir Shmuel, Dr." <amir.shmuel(a)mcgill.ca> To: "Amir Shmuel, Dr." <amir.shmuel(a)mcgill.ca> Subject: Resting-State and Brain Connectivity 2018: Added Events & Submission Deadline External Email - Use Caution Resting State and Brain Connectivity 2018 in Montreal: (1) We have added a RECEPTION and a “SCIENTIFIC MATCHING and DATING” event: meet a colleague that can advise on your modeling, analysis, machine learning etc. (September 26). (2) We have added a satellite workshop on how to incorporate machine learning and/or deep learning in your data analysis (September 29). Abstract submission deadline is August 1st. http://restingstate.com/2018/satellite-symposia/ Amir Shmuel Chair of the organizing committee Resting State and Brain Connectivity 2018 http://restingstate.com/2018/wp-content/uploads/2017/06/resting-state-logo-…

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Transform using talairach.m3z for submillimeter data
by Ren, Jianxun 26 Jul '18

26 Jul '18

Hi FS experts, I reconstructed several 0.75mm structural images using recon-all v6 with highres flag successfully and everything looks fine. Now, I want to transform structural images (norm.mgz, 0.75mm3, 320^3) to the common space (MNI305, 1mm3, 255^3 for freesurfer) using mri_vol2vol with mri/transforms/talairach.m3z, however the result looks wired with distorted shape and wrong centroid. I also attempt to run mri_convert with "-at" flag. The output looks fine and the resolution keeps the same with input, i.e. 0.75mm3. So I suppose the problem of using mri_vol2vol is the wrong "targ" reference, which should be a high resolution MNI305, But I can't find it. Could you tell me if my understanding is right or not? If it's right, where can I find the high resolution MNI305 template? There are the commands I used: mri_vol2vol --mov norm.mgz --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z transforms/talairach.m3z --noDefM3zPath --o norm_mni305.nii.gz --interp trilin mri_convert -at transforms/talairach.m3z norm.mgz norm_mni305.nii.gz -oc 0 0 0 Best, Jianxun

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26 Jul '18

External Email - Use Caution Dear Freesurfer experts, I have mask in MNI152 space. I would like to register this mask to fsaverage. How can I do this registration. I am thinking of "mri_vol2surf" as follows: mri_vol2surf --mov mask.nii --mni152reg --regheader fsaverage --o mask_fsaverage.nii Is this command correct? Thank you for your valuable guidnace John

2 4

Data sets with enlarged ventricles
by Khoi Mai 26 Jul '18

26 Jul '18

External Email - Use Caution Hello, We are trying to run two subjects through recon-all. The kicker is that these two have very large ventricles and we have been stuck at mris_fix_topology (the script reports about 100-ish defects for each). We use HPC to run the analyses but even with a walltime of 96 hours each, both subjects were unable to be finished within that time frame. My question is that is there any way to improve mris_fix_topology runtime? Subject 1: Subject 2: Thank you for your help. Best, Khoi

2 2

mri_glmfit
by Piero Chiacchiaretta 26 Jul '18

26 Jul '18

External Email - Use Caution Dear FS group, I would like to restrict mri_glmfit analysis, on FS-FAST outputs, to the cerebellum. Thus, I’m using —mask, adding the mask of cerebellum. To this aim I can obtain it using mri_binarize. Do you agree? mri_binarize --i ... --match 8 --o Left_Cerebellum.nii.gz mri_binarize --i ... --match 45 --o Right_Cerebellum.nii.gz Which is the correct input? aparc+aseg in fsaverage? In which dimension? mri.2mm? mri? Thanks Piero

2 1

brain parenchymal fraction
by Barletta, Valeria 26 Jul '18

26 Jul '18

Dear Freesurfers, I need to extract the brain parenchymal fraction to check brain atrophy in my patients. The BPF is defined as "the ratio of brain parenchymal tissue volume to the total volume contained within the brain surface contour". In the text file aseg.stats, I found this info: # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1052408.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1032104.000000, mm^3 # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1030608.836503, mm^3 Can I extract the BPF from those, or is any of them the BPF? Thank you, Valeria

2 2

Yeo-2011 individual ROIs
by Ehsan Tadayon 26 Jul '18

26 Jul '18

External Email - Use Caution Hi, Is there an easy way to sub-parcellate each network in Yeo-2011 (for instance network 7) into several clusters (ROIs) for an individual subject? thanks Ehsan.

3 2

Longitudinal Processing - Retaining Manual Edits
by KALEY E ELLIS 26 Jul '18

26 Jul '18

External Email - Use Caution Dear FreeSurfer Developers, We are using your longitudinal processing pipeline (version 6.0) for our study (n=140, 3 timepoints). Our scanner was upgraded a year ago and the a filter was used on the raw images to adjust for hyperintensities in the images due to using a multi-channel coil. At this point, our bases have already been processed and consist of three timepoints with a mix of filters: T1 no filter, T2 no filter, T3 with filter. Since we have invested many resources into the manual editing process, we want to try to retain all the manual edits that have been done to the base. We still have the original scan and the filtered scan for each subject. We have some ideas on how we might be able to retain the edits, but would you be able to provide input regarding whether this seems reasonable? Your feedback is greatly appreciated! Plan A: 1) Create a new T3 cross-sectional with the correct nifti 2) Run recon-all on the existing base Q: Will this retain the previous manual edits AND incorporate the new cross-sectional image? Plan B: 1) Create a new T3 cross-sectional with the correct nifti 2) Create a new base Q: Is it possible to transfer data from old manual edits to a new base? If so, how? Thank you! Kaley Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

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