Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

segmentHA_T1.sh
by Daniel Callow 01 Apr '19

01 Apr '19

External Email - Use Caution Hello, I have finished running segmentHA_T1.sh on my data and have gotten all the .mgz and .txt files in my mri folder. I would like to collect all the hippocampal volumes and get them into a table to run stats on. When reading the documentation it says that It will also produce files in the stats folder called hipposubfields.[lr]h.T1.v2x.stats and amygdalar-nuclei.[lr]h.T1.v2x.stats. These can be compiled across subject with, eg, asegstats2table --statsfile=hipposubfields.lh.T1.v21.stats --tablefile=hipposubfields.lh.T1.v21.dat ... However, the stats folders for my subjects do not have these files in the stats folder. Just the usual aseg.stats lh.aparc.a2009s.stats lh.aparc.DKTatlas.stats lh.aparc.pial.stats lh.aparc.stats lh.BA_exvivo.stats lh.BA_exvivo.thresh.stats lh.curv.stats lh.w-g.pct.stats rh.aparc.a2009s.stats rh.aparc.DKTatlas.stats rh.aparc.pial.stats rh.aparc.stats rh.BA_exvivo.stats rh.BA_exvivo.thresh.stats rh.curv.stats rh.w-g.pct.stats wmparc.stats Is there a way to get the correct stats files in my stats folder so I can use the suggested command? Or is there a way to extract the information from the .txt files? Any help you can provide would be greatly appreciated! *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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Custom Colormap
by Emanuel Alvaredo 01 Apr '19

01 Apr '19

External Email - Use Caution Hello! I would like to ask you about customs colormaps. I have created my own FreeSurferColorLUT.txt and I would like configure the color map using command line. Is it possible? Thanks in advance. Emanuel

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

29 Mar '19

External Email - Use Caution Hello, To add to my original post it seems the issue is I am not able to look at these merged images or that the HBT file write out seems to be wrong? I don't know how to post a picture to the listserve so someone can determine if I am just looking at it incorrectly in freeview? Any help is greatly appreciated! 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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VT images from pmod to freesurfer
by Donatienne Van Weehaeghe 29 Mar '19

29 Mar '19

External Email - Use Caution Dear, I encountered a problem when going from pmod to freesurfer. I made Vt images in pmod using the logan plot, then I used the following commands to convert them to freesurfer space: #flirt -noresample -in /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii -ref /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/T1-2mm_skullstripped.nii.gz -applyxfm -init /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUV.lrrev_lin_T1.mat -out /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii #3dresample -master /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/occipital.nii.gz -inset /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii -prefix /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii Then I did partial volume correction using this command: #mri_gtmpvc --i /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii --reg Vt.reg.lta --psf 5 --seg /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz --default-seg-merge --auto-mask 5 0.01 --rbv --o /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg --no-rescale --threads 8 Then I did surface projection: #mri_vol2surf --mov /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz --reg /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta --hemi lh --projfrac 0.5 --o /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/lh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz --cortex --trgsubject fsaverage #mri_vol2surf --mov /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz --reg /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta --hemi rh --projfrac 0.5 --o /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz --cortex --trgsubject fsaverage followed by smoothing, concatening and then a group comparison. However then I obtained the following error: ERROR: cannot find /usr/local/freesurfer/stable6_0_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/pos/th13/mc-z.csd Kind regards Donatienne

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Group X Time Interaction in Qdec
by brain health 29 Mar '19

29 Mar '19

External Email - Use Caution *What is the best way to run a whole- brain Group (intervention group, control group) x Time (Pre, post) interaction via QDEC? (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_free… <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_free…>)* *Thanks!*

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