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30084 discussions

Is subcortical segmentation reliable when cortical segmentation fails?
by Fredrik 10 Dec '19

10 Dec '19

External Email - Use Caution Hi FreeSurfer experts, In our data, we have a sample of older people with brain athrophy. This influences the cortical segmentation, where it can take into consideratin the skull, and/or leave out grey matter. My question regards the subcortical segmentation in such cases: Is it reliable to use the subcortical segmentation when the cortical segmentation clearly fails? Thanks, Fredrik Magnussen

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intensity map
by a Chinese reader 10 Dec '19

10 Dec '19

External Email - Use Caution Dear Freesurfer experts,I have some questions about intensity map: 1. If I would like to get intensity maps of WM, which were created at 1 mm below the white surface, and the GM were taken at half of the thickness of the cortex. which commands I can use. 2. How to use the command line to get the Grey-matter tissue intensity at 10% up to 60% of the distance from the white matter to the pial surface. 3. Then, how to get the WM/GM intensity maps use the above values. Best regards, Zhang Xia

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TRACULA question: Preprocessing exited with ERRORS
by Miguel Ángel Rivas Fernández 09 Dec '19

09 Dec '19

External Email - Use Caution Dear Freesurfer experts, I am a beginner in the use of TRACULA. I tried to run the preprocessing step of the trac-all command and it seems that all have worked fine. However, at the end of the command TRACULA finished with an error. This is the final output tkregister2 --mov /Applications/freesurfer_dev/freesurfer/subjects/TUTORIAL_DATA/4220/4220/4220/dmri/brain_anat_orig.nii.gz --targ /Applications/freesurfer_dev/freesurfer/subjects/TUTORIAL_DATA/4220/4220/4220/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Applications/freesurfer_dev/freesurfer/subjects/TUTORIAL_DATA/4220/4220/4220/dmri/xfms/anatorig2anat.mat --reg /Applications/freesurfer_dev/freesurfer/subjects/TUTORIAL_DATA/4220/4220/4220/dmri/xfms/anat2anatorig.dat tkregister2: Command not found. Darwin rmnlab1.inv.usc.es 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Mon Dec 9 22:00:14 CET 2019 You can find the configuration file and the trac-all.log file in attached. Best regards, -- *Miguel Ángel Rivas Fernández*

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Recon-all
by Gwang-Won Kim 09 Dec '19

09 Dec '19

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"Bad CPU type in executable" error
by Abhi Jaywant 09 Dec '19

09 Dec '19

External Email - Use Caution Hi, I am trying to run the tkregister2.bin script and receive the following error: Bad CPU type in executable. I see that this question was asked some time back and it sounded like it might be a Mac OS version issue? I am running macOS Catalina 10.15.1 and Freesurfer version 6 (freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c) Thank you, Abhi -- Abhishek Jaywant, Ph.D. Assistant Professor of Neuropsychology, Weill Cornell Medicine Assistant Attending Psychologist, NewYork-Presbyterian Hospital

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Vertex-wise ROI extractions on the surface
by DeCross, Stephanie N. 09 Dec '19

09 Dec '19

Hi, How can I extract functional data (percent contrast) from an aparc ROI on the surface on a vertex-wise basis (i.e. not one value averaged across the whole ROI, but one value per vertex inside the ROI for a given contrast)? Funcroi-config/funcroi-sess/funcroi-table-sess seem to only provide values averaged across the whole ROI. In other analysis pipelines, for a voxel-wise extraction it looks like I would use $ fslmeants -i <input 4D nii> -o <output.txt> -m <3D mask nii> --showall but I’m not sure how to do this on the surface. Thank you, Stephanie DeCross

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fsaverage for externally preprocessed subjects.
by Alvarado,Luis R 09 Dec '19

09 Dec '19

External Email - Use Caution Hi all, I have a couple of questions regarding fsaverage: 1. Is this file updated every time a new subject is process with recon-all? 2. If I obtain externally preprocessed datasets (e.g., from the 1000 Functional Connectomes Project) should I register those subjects to my local fsaverage? * Ultimately, I would like to conduct an ROI analysis of the differences between normative data from a large online biobank and locally imaged patient population. The workflow for such analysis recommended on (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI) suggests to draw ROI labels directly on fsaverage (a template to which all subjects run with FreeSurfer have been registered to) and then use the mri_label2label command to map the label to individual subjects. Would this work for both locally and externally preprocessed groups? Thank you, Luis R. Alvarado Ph.D. Candidate Department of Anatomical Sciences and Neurobiology University of Louisville School of Medicine Kentucky Spinal Cord Injury Research Center 220 Abraham Flexner Way, Suite 1500 Louisville, KY 40202

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Reconstruction on BLADE sequences
by Funk, Quentin 09 Dec '19

09 Dec '19

External Email - Use Caution Freesurfer experts, We're attempting to get some reconstructions on MRI's for very advanced alzheimer's subjects. Many of these subjects have pretty extensive motion artifacts in their acquisitions. There has been some work with the so-called BLADE sequences to eliminate motion. Indeed, some of the blade sequences produce fairly good contrast. But these acquisitions have slices that aren't normalized for brightness and I think this complicates the reconstruction--see ( https://imgur.com/ZWhBlcm ) for an example. It seems like we should be able to perform some kind of slice-wise normalization to fix this, but I can't see a good way to do that with the freesurfer tools. Any advice would be greatly appreciated! Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003<tel:713-363-9003> Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas and among the top 20 hospitals nationwide. Houston Methodist is the only nationally ranked Honor Roll hospital in the state and is designated as a Magnet hospital for excellence in nursing. houstonmethodist.org | twitter.com/MethodistHosp | facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Thalamic nuclei segmentation
by Miguel Ángel Rivas Fernández 08 Dec '19

08 Dec '19

External Email - Use Caution Dear Freesurfer devs, I tried to run the thalamic nuclei segmentation (T1 and T2 as input) using the freesurfer dev version and the terminal gave to me the following error rmnlab1:~ neucoga$ segmentThalamicNuclei.sh 4001 /Applications/freesurfer_dev/freesurfer/subjects/4001/mri/orig/T2.nii THALAMUS BBREGISTER_MODE t2 Setting ITK threads to 1 #-------------------------------------------- #@# Thalamic Nuclei processing domingo, 8 de diciembre de 2019, 20:55:24 CET ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer_dev/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer_dev/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer_dev/freesurfer/MCRv84//sys/os/maci64:/Applications/freesurfer_dev/freesurfer/lib/gcc/lib:/Applications/freesurfer_dev/freesurfer/lib/gcc/lib Error using SegmentThalamicNuclei (line 138) Additional volume does not exist 255 Darwin rmnlab1.inv.usc.es 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64 Thalamic nuclei exited with ERRORS at domingo, 8 de diciembre de 2019, 20:55:31 CET For more details, see the log file /Applications/freesurfer_dev/freesurfer/subjects/4001/scripts/thalamic-nuclei-BBREGISTER_MODE.log Is the command right? I think that I have followed correctly the instructions of the website. Best regards, -- *Miguel Ángel Rivas Fernández*

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Re: [Freesurfer] Hippocampus subfields outputs missing
by Iglesias Gonzalez, Juan E. 06 Dec '19

06 Dec '19

Dear Naveed, You need the development version; these files are not given by FreeSurfer 6.0. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Muhammad Naveed Iqbal Qureshi <mniqureshi(a)hotmail.com> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, 6 December 2019 at 13:44 To: Freesurfer maillist <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampus subfields outputs missing External Email - Use Caution Hi I ran the following command not the subject on HPC module load matlab/r2013a module load freesurfer/6.0.0 source $FREESURFER_HOME/SetUpFreeSurfer.sh fixup_mni_paths recon-all -all -no-isrunning -s /hpf/projects/glongoni/ADHD-200/$file -subjid ADHD-${PBS_ARRAYID} -hippocampal-subfields-T1 -sd /hpf/projects/glongoni/ADHD-200/ -openmp 8 in the output directory I get only following files for both left and right hemisphere lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz lh.hippoSfLabels-T1.v10.mgz lh.hippoSfVolumes-T1.v10.txt How can I get following files? lh.hippoAmygLabels-T1.v21.CA.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.v21.CA.mgz lh.hippoAmygLabels-T1.v21.FS60.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.v21.HBT.FSvoxelSpace.mgz I try to find this command but it is not available in my installation segmentHA_T1.sh Regards, Naveed

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