Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

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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nu_correct: Command not found
by Ian Hardingham 29 Mar '19

29 Mar '19

External Email - Use Caution Hello all. I am attempting to run recon-all in a docker container. I have a set of commands to set up the system, and on my local machine (Ubuntu) it works fine. However on the docker container (also Ubuntu) I get nu_correct: Command not found. I imagine there is some software that is required that I haven't installed on the container image - does anyone have any idea what it might be? 1. I have run these commands: source /usr/local/freesurfer/SetUpFreeSurfer.sh export PATH=/usr/local/freesurfer/bin:PATH=/usr/local/freesurfer/mni/bin:$PATH 2. I have set FREESURFER_HOME Attached at the end is some output from both failing and successful runs. 3. nu_correct exists in freesurfer/mni/bin 4. Perl is present and correct on both systems. Thank you in advance, Ian FAILING OUTPUT: #-------------------------------------------- #@# Talairach Thu Mar 28 14:12:31 UTC 2019 /subjects/FS_subj_001/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /subjects/FS_subj_001/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 40ed7e79aa5d 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 GNU/Linux Thu Mar 28 14:12:32 UTC 2019 nu_correct: Command not found. SUCCESSFUL OUTPUT: #-------------------------------------------- #@# Talairach Thu Mar 28 14:33:45 GMT 2019 /home/ian/subjects/FS_subj_001/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/ian/subjects/FS_subj_001/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux ian-Sabre-17WV8 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Thu Mar 28 14:33:45 GMT 2019 Program nu_correct, built from: -- Ian Hardingham

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Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: [WARNING: UNSCANNABLE EXTRACTION FAILED]talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***
by Bruce Fischl 28 Mar '19

28 Mar '19

Hi Chhavi can you post this type of question to the FS list (which I'll cc on my response)? You only need to give recon-all a single dicom slice that is from the correct series. If the rest of the dicoms are in the same dir we will find them and properly assemble the volume from them. cheers Bruce On Mon, 25 Mar 2019, Chhavi Yadav wrote: > > External Email - Use Caution > > Hi Bruce, is there a way I can do recon-all -autorecon1 for all the slices for a subject without > using the -i flag? I mean I do not want to mention every single slice's name in the command. > > On Mon, Mar 25, 2019 at 12:59 PM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > On Mon, 25 Mar 2019, Chhavi Yadav wrote: > > > > > External Email - Use Caution > > > > Okay got it. So I will still writerecon-all -autorecon1 -i new.dcm -s outnew > > Just that new.dcm should be in the folder with the other slices. Is that correct? > > > > Also some of my slices are noisy, just ears or completely black. > > Sorry for sending to the list. > > > > Thanks for your help.. > > Chhavi > > > > > > On Mon, Mar 25, 2019 at 12:44 PM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > Hi Chhavi > > > > if you look in the recon-all.log file you will see the volume dimensions > > as: > > > > Image information > > RunNo 4 > > SeriesNo 5 > > ImageNo 56 > > NImageRows 256 > > NImageCols 240 > > NFrames 1 > > SliceArraylSize 1 > > IsMosaic 0 > > ImgPos 36.2753 164.5335 99.2486 > > VolRes 1.0000 1.0000 1.2000 > > VolDim 240 256 1 > > Vc -0.0000 -1.0000 0.0000 > > Vr -0.0000 -0.0000 -1.0000 > > Vs -1.0000 -0.0000 0.0000 > > VolCenter 35.6753 44.5335 -28.7514 > > TransferSyntaxUID 1.2.840.10008.1.2.1 > > > > > > so it is only a single slice. You need to have the entire dicom series in > > the same directory so that we can find the other slices > > cheers > > Bruce > > > > > > On Mon, 25 Mar 2019, > > Chhavi Yadav wrote: > > > > > > > > External Email - Use Caution > > > > > > attached is a sample on which it fails.I just do recon-all -autorecon1 -i > new.dcm -s outnew > > > > > > Is this okay? Also attached is the log. > > > I haven't tried all. > > > > > > On Mon, Mar 25, 2019 at 12:26 PM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > > > did all of them fail? That seems unlikely. Our failure rates are usually > > > pretty low (less than a couple of percent). If they are all failing > > > something else is wrong > > > > > > > > > On Mon, 25 Mar 2019, Chhavi Yadav wrote: > > > > > > > > > > > External Email - Use Caution > > > > > > > > HI Bruce,Thanks for your email. > > > > I actually have 3500 files. So cant do transform on them manually. Any > other way? > > Like > > > downloading the > > > > previous version of freesurfer? > > > > Chhavi > > > > > > > > On Mon, Mar 25, 2019 at 10:56 AM Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> wrote: > > > > Hi Chhavi > > > > > > > > the automated Talairach transform creation can sometimes fail, > > > > particularly in the presence of very large ventricles or lots of > > > > damaged white matter or > > > > both. We have a tutorial on checking and correcting it here: > > > > > > > >https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard… > l_Tala > > ir > > > > > > >ach-5Ffreeview&d=DwIDaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKb > HktL7Q > > rJ > > > > > > > JELPuLToS-_5lkY&s=LpBDOkEFGzHx0owj2xszaOGP5m2RG6gsMN9vq30fOBU&e= > > > > > > > > cheers > > > > Bruce > > > > > > > > On > > > > Mon, 25 Mar 2019, Chhavi Yadav wrote: > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > Hi,I am a beginner to freesurfer. Never used it before. > > > > > Currently I am working on some dicoms from ADNI that I want to > preprocess. > > > > > But I am getting this 'talairach_afd: Talairach Transform: > > transforms/talairach.xfm > > > > ***FAILED*** ' error. > > > > > I am attaching the error log and other files for your > reference. Please > > help me > > > out. > > > > > > > > > > Regards, > > > > > Chhavi > > > > > > > > > >_______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > >https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… > reesur > > fe > > > > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKbHktL7QrJJELPu > LToS-_ > > 5l > > > > > > > kY&s=bKPWvTI6mhmqTDXPcjuZiBrd9LczeJVcqb47rKN8Lvg&e= > > > > > > > > > > > >_______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > >https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… > eesurfe > > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=rJfQ3hIQWvKqc6fZyhUQKNa911LU20WsF_ > c8g2VP7 > > > > > LM&s=DgN0IsA48XVzgAFsDxvg5H2euo0dyxsaX8Y4v0koRB0&e= > > > > > > > > >_______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > >https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… > surfe > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=0en6N_H-HDM_3l0J3ZVznuaBX1sw-F8kv1S2 > TCg3F > > G0&s=9Qp6YLWJpuHPgkqfW-Sv0N-cNqEect_0FX7_G-R_V10&e= > > > > > > > > >

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