Freesurfer March 2019

freesurfer@nmr.mgh.harvard.edu

114 participants
172 discussions

regions of Yeo 17 networks in fast
by stdp82＠virgilio.it 10 Apr '19

10 Apr '19

External Email - Use Caution Hi list, I'd like to use the regions included in Yeo 17 networks (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parc…) in FS-FAST. Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid). Thanks Stefano

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freesurfer longitudinal issue
by maxime GUILLAUME 10 Apr '19

10 Apr '19

External Email - Use Caution Dear freesurfer experts, I am performing a longitudinal study (2 time points, 1 year apart) in patients with Multiple Sclerosis using freesurfer 6.0. After following the tutorial for the CROSS, the BASE (where I only performed few manual edits of the surfaces) and the LONG steps, I am facing a problem with the results of the longitudinal pipeline: If I overlay the final surfaces of the different time points (the white and pial surfaces of the LONG step) on the BASE template, there are major differences between the two time points (see figure attached). This happened only on a subset of my subjects. One of our collaborators in this study suggested that this might be because the patient was positioned differently in the two time points, in particular with respect to the z axis (and indeed the major differences between the two surfaces are in the topmost area of the brain). Does anybody have experienced the same problem? And how can I correct for it? Thank you in advance for your help. (*in the capture surfaces of the first visit are in yellow and in green for the second visit)

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mris_preproc not running
by Sims, Sara A (Campus) 02 Apr '19

02 Apr '19

External Email - Use Caution Hello! I have 786 subjects that I am trying to do a paired difference analysis using mri_glm. I am getting stuck at the mris_preproc stage. I have tried running it on a handful of subjects and it works wonderfully. However, when I run it on all the subjects it outputs an empty file. I think part of my problem is that I am having to do 1572 flags to enter all the subjects files (which I made a script to create, I did not hand type them). Is there a better way to do this? Do I just have too many subjects? This is what I have that isn’t working: mris_preproc --target fsaverage --hemi lh --isp $in/${network}/100206.${run1}/lhsurf.mgh --isp $in/${network}/100206.${run2}/lhsurf.mgh --isp $in/${network}/100307.${run1}/lhsurf.mgh --isp $in/${network}/100307.${run2}/lhsurf.mgh ……. --out $out/preproc_${network}_${pair}/lh.paired-diff.${network}_${pair}.mgh --f $sublist --paired-diff --no-cortex-only Thanks for the help! Sara Sims

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(no subject)
by Giuliana Klencklen 02 Apr '19

02 Apr '19

External Email - Use Caution Hi FS experts, I use tksurfer (e.g., tksurfer fsaverage/ lh inflated -gray) to open the overlays (i.e., something.sig.cluster.mgh) I generated with the permutation simulation correction. It goes perfectly well for most of them expect for some, where the overlay does not show at all the significant clusters summarized in the something.sig.cluster.summary. I run the mri_glmfit-sim command again but the problem persists. Does anyone have a clue about what is going wrong? Many thanks, Giuliana Klencklen -- Giuliana Klencklen, Ph.D. Helen Wills Neuroscience Institute University of California, Berkeley 118 Barker Hall Berkeley, CA 94720-3190 510-395-0040 giuliana.klencklen(a)berkeley.edu

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trouble converting between .mgz and .nii.gz
by JD Knotts 01 Apr '19

01 Apr '19

External Email - Use Caution Hello experts, As a sanity check in a pipeline I'm running I tried converting an atlas file containing visual ROIs from .mgz to .nii.gz and then immediately converting the resulting .nii.gz file back to .mgz: mri_convert lh.atlas.mgz lh.atlas.nii.gz --reslice_like subject_t1.nii.gz --resample_type nearest --out_data_type int --no_scale 1 mri_convert lh.atlas.nii.gz lh.atlas_reconverted.mgz --reslice_like subject_t1.nii.gz --resample_type nearest --out_data_type int --no_scale 1 Something is getting lost in this conversion and reconversion, because when I run the following two lines (to generate a label for V1) on the two different .mgz files, the original file correctly results in the identification of 1591 label voxels, while the converted/reconverted file incorrectly results in the identification of 111 label voxels, none of which overlap with the 1591 correct voxels: mri_vol2surf --src mri/lh.atlas.mgz \ --src_type FLOAT \ --srcreg mri/register.dat \ --hemi lh \ --surf white \ --o mri/lh.atlas.mgh mri_cor2label --c mri/lh.atlas.mgh \ --id 1 \ --surf SubID lh \ --l label/lh.V1_ventral.label Any feedback on where I'm going wrong here would be greatly appreciated! Thanks for your time, JD Knotts 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Platform: Mac OSX 10.11.6 3) Darwin Jeffreys-MacBook-Pro.local 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 23 18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64 -- Doctoral Candidate, Cognitive Neuroscience Department of Psychology University of California, Los Angeles

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Postdoctoral position available at SCAN lab, University of Arizona
by Sahil Bajaj 31 Mar '19

31 Mar '19

External Email - Use Caution Hello everyone, We have an opening for a post-doctoral fellow with an interest and/or background in emotional/social processing, emotional intelligence, emotional/social cognition, psychology and/or social psychology. Here, I am attaching the PDF of the job posting and also sharing the link to this job application so that you can apply directly: https://uacareers.com/postings/35999 . More details about our lab: https://scanlab.arizona.edu/ For any questions, please email our lab manager, Emily Taylor: emilytaylor(a)psychiatry.arizona.edu Thank you ! Best, Sahil

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Partial volume correction for aseg.mgz files
by Song, Da-Yea 29 Mar '19

29 Mar '19

External Email - Use Caution Hello, I'm trying to extract regions (mri_extract_label) of interest from the aseg.mgz files and compare them to our manual segmentations. I've warped these ROI masks onto our native space. I've noticed on the forum that there were mentions of discrepancies in the volumes from aseg.mgz and aseg.stats due to partial volume correction. If I were to calculate the volume using the ROI extracted masks (that have been warped on to the native space), how can I calculate for partial volume correction? Any suggestions would be greatly appreciated! Thank you, Da-Yea ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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segmentHA_T1_long.sh HBT issue
by Daniel Callow 29 Mar '19

29 Mar '19

External Email - Use Caution The issue was that I was using the freesurfer 6.0 version of freeview and not the development version. Thanks for your help Eugenio! Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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segmentHA_T1_long.sh HBT issue
by Daniel Callow 29 Mar '19

29 Mar '19

External Email - Use Caution Hello, I have run *segmentHA_T1_long.sh from the developer freesurfer version and am looking to segment and visualize the head body and tail of the left and right hippocampus.* *However, when looking at the lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz and other files for each subject I see only amygdala and subfield segmentations. How do I use the outputs to create a head body and tail segmentation that I can visualize and extract values from?* *Best,* *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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petsurfer
by 妮 29 Mar '19

29 Mar '19

External Email - Use Caution Hi developers,I am using the petsurfer now to do the PVC for my dynamic analysis, however there is something error happened. Here is my commends: mri_coreg --mov fICL161363_000006_1_BU99008_9744_merged_00015.nii --ref fICL161363_000006_1_MRI_9746_series_2_MPRAGE_ADNI_P2.nii --reg template.reg.lta --s subject6 mri_gtmpvc --i fICL161363_000006_1_BU99008_9744_merged.nii --reg template.reg.lta --psf-col 9.2 --psf-row 10.5 --psf-slice 14.6 --seg subject6/mri/gtmseg.mgz --default-seg-merge --mgx .01 --o gtmpvc.output --km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale the coreg was ok, however the gtmpvc is not ok, here is the lines show my terminal, could you tell me what's the problem and how to fix it, Thanks so much for help me. Loading input fICL161363_000006_1_BU99008_9744_merged.nii WARNING: niiRead(): unknown time units 0 in /Volumes/NIU20/analysis/volumetric_FS/trail/fICL161363_000006_1_BU99008_9744_merged.nii INFO: using NIfTI-1 qform done loading input 28 frames $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ setenv SUBJECTS_DIR /Volumes/NIU20/analysis/volumetric_FS/trail cd /Volumes/NIU20/analysis/volumetric_FS/trail mri_gtmpvc --i fICL161363_000006_1_BU99008_9744_merged.nii --reg template.reg.lta --psf-col 9.2 --psf-row 10.5 --psf-slice 14.6 --seg subject6/mri/gtmseg.mgz --default-seg-merge --mgx .01 --o gtmpvc.output --km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale sysname Darwin hostname cengzhoudeMacBook-Air.local machine x86_64 user cengzhou vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 4 avail.processors, using 1 Creating output directory gtmpvc.output Loading seg for gtm subject6/mri/gtmseg.mgz Loading seg ctab subject6/mri/gtmseg.ctab Reading subject6/mri/gtmseg.lta ERROR: LTAconcat(): LTAs 0 and 1 do not match LTA 0 ------------------- type = 0 # LINEAR_VOX_TO_VOX nxforms = 1 mean = 0.0000 0.0000 0.0000 sigma = 10000.0000 1 4 4 5.000000000000000e-01 0.000000000000000e+00 0.000000000000000e+00 4.875000000000000e+01 0.000000000000000e+00 5.000000000000000e-01 0.000000000000000e+00 3.475000000000000e+01 0.000000000000000e+00 0.000000000000000e+00 5.000000000000000e-01 1.775000000000000e+01 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 src volume info valid = 1 # volume info valid filename = /Volumes/NIU20/analysis/volumetric_FS/trail/subject6/mri/apas+head.mgz volume = 316 440 438 voxelsize = 5.000000000000000e-01 5.000000000000000e-01 5.000000000000000e-01 xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00 zras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 cras = 2.500000000000000e-01 -7.500000000000000e-01 -1.675000000000000e+01 dst volume info valid = 1 # volume info valid filename = /Volumes/NIU20/analysis/volumetric_FS/trail/subject6/mri/apas+head.mgz volume = 256 256 256 voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00 zras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 cras = 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 subject subject6 fscale 0.150000 LTA 1 ------------------- type = 0 # LINEAR_VOX_TO_VOX nxforms = 1 mean = 0.0000 0.0000 0.0000 sigma = 10000.0000 1 4 4 1.490079522132874e+00 -1.009208321571350e+00 -9.591113924980164e-01 8.742171478271484e+01 9.481825828552246e-01 1.776931047439575e+00 -3.772042095661163e-01 -4.950695037841797e+01 1.042477130889893e+00 -1.736743301153183e-01 1.714007139205933e+00 2.799880599975586e+01 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 src volume info valid = 1 # volume info valid filename = fICL161363_000006_1_BU99008_9744_merged_00015.nii volume = 128 128 82 voxelsize = 2.050889968872070e+00 2.050889968872070e+00 2.000000000000000e+00 xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 zras = 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 cras = 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 dst volume info valid = 1 # volume info valid filename = fICL161363_000006_1_MRI_9746_series_2_MPRAGE_ADNI_P2.nii volume = 160 240 256 voxelsize = 1.000000953674316e+00 1.000000000000000e+00 1.000000000000000e+00 xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 zras = -0.000000000000000e+00 -0.000000000000000e+00 1.000000000000000e+00 cras = 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 subject subject6 fscale 0.150000 -------------------------- ERROR: LTAconcat() mri_gtmpvc exited with errors

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Freesurfer March 2019