Freesurfer May 2018

freesurfer@nmr.mgh.harvard.edu

117 participants
167 discussions

Extracting DTI/NODDI data from hippocampal subfields
by Mark Wagshul 02 May '18

02 May '18

External Email - Use Caution Hi. I am just getting my feet wet with running my subjects through the Freesurfer processing stream, so the following question night be a bit trivial (I hope): I have run qvlSegmentHippocampal subfields on one of my subjects, and it completed just fine with what seem to be the appropriate outputs in the subject's mri folder. I have another 100 subjects to run, but want to make sure I can accomplish what I would like to on this subject first. The images which I see are sub-images, i.e. these have fewer voxels compared to the original image, but in the native T1 space resolution (= 1 mm3). I would now like to register the subfields in the native space (my DTI/NODDI maps are already registered into this space), to obtain mean values within each subfield. How can I transform these sub-field images back into the native T1 space, or is there a method within Freesurfer to perform the math (e.g. similar to fslmaths)? Thanks, Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einstein.yu.edu<mailto:mark.wagshul@einstein.yu.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

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using diffusion for tracula, but with surfaces from a different MR sessions
by Alexopoulos, Dimitrios 02 May '18

02 May '18

External Email - Use Caution We have acquired data on a few kids and have generated nice surfaces, however, the diffusion data we acquired (102 directions and AP/PA distortion maps) were suspect due to motion and results from Tracula were not ideal. We have since brought these kids back for a repeat scan, but only acquired the diffusion sequences, and no structural T1. Can we use the original surfaces/output as input to tracula with the DTI data from the repeat MR session? Jim "The materials in this email are private and may contain Protected Health Information. 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 email in error, please immediately notify the sender via telephone or return email." ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Difference between freesurfer home folders
by Hurtado, Aura Maria 02 May '18

02 May '18

Hi all, I’m digging into data that was reconned a while ago. I see in the recon-all.done files and some say: CMDPATH /usr/local/freesurfer/stable6/bin/recon-all and others say: CMDPATH /usr/local/freesurfer/stable6_0_0/bin/recon-all Is there a difference between the recon-all commands in the stable 6 and the stable6_0_0 freesurfer folders? Thanks, Aura M.

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Re: [Freesurfer] mri_vol2surf warning
by Douglas N. Greve 02 May '18

02 May '18

And what is the voxel resolution of the input to mri_vol2surf? On 05/02/2018 03:35 PM, Rachel Bencic wrote: > > > Hello, > > The voxel resolution of the unwarped mov volume used in bbregister was: > > voxel sizes: 3.750000, 3.750000, 5.000000 > > So the reported values in the warning appear correct. > > Rachel > > > > On 05/02/2018, Douglas Greve wrote: > > When you ran bbregister, what was the voxel resolution of the mov volume? > On 05/02/2018 01:28 PM, Rachel Bencic wrote: > > > > > > Hello FreeSurfer Developers, > > > > I'm attempting to resample beta weights generated from AFNI’s > > 3dDeconvolve command to individual subjects’ cortical surfaces. Prior > > to running 3dDeconvolve, I ran bbregister to coregister subjects’ > > (unwarped) functional data to their T1 anatomical scans and to > > generate a registration file to be used in the mri_vol2surf command. > > > > However, I get the following warning when I run the mri_vol2surf command: > > > > WARNING: the voxel resolution in the source volume (3.75, 3.75, 3.75) > > differs from that listed in the registration file (3.75, 3.75, 5) > > > > I've searched the list and came across a potentially similar case from > > Apr. 26, 2011 (SUBJECT: (no subject), AUTHOR: Kevin Bickart), which > > included the following advice: > > > > Hi Kevin, you can ignore that warning. The values in the registration > > > > file are not correct. > > > > doug > > > > I thought I would reach out to inquire as to whether this is still the > > case (i.e., that this warning can be ignored) or if it might be a more > > serious issue? I will add that mri_vol2surf did appear to run > > successfully (i.e., it did not error out) and provided a .mgh file as > > output. > > > > In case it is helpful, as a next step I plan to convert the .mgh file > > to an ASCII file to extract the time series. Ultimately, I plan to run > > graph analyses on the time series data. > > > > Any feedback you have would be greatly appreciated. > > > > Rachel > > > > 1) FreeSurfer version: freesurfer_6.0_x86_64 > > > > 2) Platform: OSX High Sierra > > > > Here is my command: > > > > mri_vol2surf --mov ../betaEPI/Betas_EPIpreproc.nii--srcreg > > ../bbregistration.dat --hemi lh --projfrac 0.5 --o ./lh.1.mgh > > > > mris_convert -c ./lh.1.mgh $parc_dir/${1}/surf/lh.white > > ../lh_ascii/lh.1.asc > > > > And the full output: > > > > srcvol = ../betaEPI/Betas_EPIpreproc.nii > > > > srcreg = ../bbregistration.dat > > > > srcregold = 0 > > > > srcwarp unspecified > > > > surf = white > > > > hemi = lh > > > > ProjFrac = 0.5 > > > > thickness = thickness > > > > reshape = 0 > > > > interp = nearest > > > > float2int = round > > > > GetProjMax = 0 > > > > INFO: float2int code = 0 > > > > Done loading volume > > > > INFO: This REGISTER_DAT transform is valid only for volumes betweenCOR > > types with c_(r,a,s) = 0. > > > > Input reg is register.dat > > > > WARNING: the voxel resolution in the source volume (3.75,3.75,3.75) > > differs > > > > from that listed in the registration file (3.75,3.75,5) > > > > -------- original matrix ----------- > > > > 0.99988-0.009970.01155-0.43638; > > > > -0.01472-0.430230.9026022.14351; > > > > 0.004030.902660.4303334.58801; > > > > 0.000000.000000.000001.00000; > > > > -------- original matrix ----------- > > > > Reading surface > > /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/lh.white > > > > Done reading source surface > > > > Reading thickness > > /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/lh.thickness > > > > Done > > > > Mapping Source Volume onto Source Subject Surface > > > > 1 0.5 0.5 0.5 > > > > using old > > > > Done mapping volume to surface > > > > Number of source voxels hit = 8657 > > > > Writing to ./lh.1.mgh > > > > Dim: 146930 1 1 > > > > srcvol = ../betaEPI/Betas_EPIpreproc.nii > > > > srcreg = ../bbregistration.dat > > > > srcregold = 0 > > > > srcwarp unspecified > > > > surf = white > > > > hemi = rh > > > > ProjFrac = 0.5 > > > > thickness = thickness > > > > reshape = 0 > > > > interp = nearest > > > > float2int = round > > > > GetProjMax = 0 > > > > INFO: float2int code = 0 > > > > Done loading volume > > > > INFO: This REGISTER_DAT transform is valid only for volumes betweenCOR > > types with c_(r,a,s) = 0. > > > > Input reg is register.dat > > > > WARNING: the voxel resolution in the source volume (3.75,3.75,3.75) > > differs > > > > from that listed in the registration file (3.75,3.75,5) > > > > -------- original matrix ----------- > > > > 0.99988-0.009970.01155-0.43638; > > > > -0.01472-0.430230.9026022.14351; > > > > 0.004030.902660.4303334.58801; > > > > 0.000000.000000.000001.00000; > > > > -------- original matrix ----------- > > > > Reading surface > > /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/rh.white > > > > Done reading source surface > > > > Reading thickness > > /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/rh.thickness > > > > Done > > > > Mapping Source Volume onto Source Subject Surface > > > > 1 0.5 0.5 0.5 > > > > using old > > > > Done mapping volume to surface > > > > Number of source voxels hit = 8681 > > > > Writing to ./rh.1.mgh > > > > Dim: 148618 1 1 >

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Starting with Neuroimaging
by Lan Naoyuki 02 May '18

02 May '18

External Email - Use Caution Hello Freesurfer experts, I am a junior in Computer Science, and am planning to join a neuroimaging lab in the summer. As far as I know, one of the projects that the lab is interested in is structural MRI analyses of bovine brains, and they would like to modify the pipeline of Freesurfer to achieve this. I have little to no experience with neuroimaging, and would like to prepare myself better before joining. My question is: is there any good resources (online courses, videos, reading, etc...) that can give me a high level picture of the analysis process? Or how to start getting into neuroimaging from a Computer Science perspective in general? Thank you for taking time to consider my questions. I apologize if they are too trivial. Best, Lan

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Differences in aseg.stats automatic results
by Fernanda Hansen P. de Moraes 02 May '18

02 May '18

External Email - Use Caution Good afternoon, I've got two types of aseg.stats results from the file automatically created from the regular script (recon-all -all). I am especially interested in the SupraTentorialVolNotVent. Here goes two examples: *Title Segmentation Statistics # # generating_program mri_segstats# cvs_version $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $# cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject SUBJ123 # sysname Linux# hostname rachael.localdomain# machine x86_64# user fernanda.hansen# anatomy_type volume# # SUBJECTS_DIR /dados1/PROJETOS/PRJ1513_GIRIFICACAO_CONTROLES/03_PROCS/PREPROC_DATA/3DT1_ALZ_FOLLOWS/DICOM_PARA_RECONVERSAO2NII/SEG# subjectname SUBJ123# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 211672.093308, mm^3# Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 216185.270458, mm^3# Measure Cortex, CortexVol, Total cortical gray matter volume, 427857.363767, mm^3# Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left hemisphere cortical white matter volume, 227845.296875, mm^3# Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right hemisphere cortical white matter volume, 227386.531250, mm^3# Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical white matter volume, 455231.828125, mm^3# Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 171469.000000, mm^3# Measure TotalGray, TotalGrayVol, Total gray matter volume, 599326.363767, mm^3# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1050908.034545, mm^3# Measure IntraCranialVol, ICV, Intracranial Volume, 1734351.873615, mm^3# SegVolFile mri/aseg.mgz Title Segmentation Statistics # # generating_program mri_segstats# cvs_version $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $# cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject SUBJ123 # sysname Linux# hostname rachael.localdomain# machine x86_64# user fernanda.hansen# anatomy_type volume# # SUBJECTS_DIR /dados1/PROJETOS/PRJ1513_GIRIFICACAO_CONTROLES/03_PROCS/PREPROC_DATA/3DT1_ALZ_FOLLOWS/DICOM_PARA_RECONVERSAO2NII/SEG# subjectname SUBJ123# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 211672.093308, mm^3# Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 216185.270458, mm^3# Measure Cortex, CortexVol, Total cortical gray matter volume, 427857.363767, mm^3# Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left hemisphere cortical white matter volume, 227845.296875, mm^3# Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right hemisphere cortical white matter volume, 227386.531250, mm^3# Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical white matter volume, 455231.828125, mm^3# Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 171469.000000, mm^3# Measure TotalGray, TotalGrayVol, Total gray matter volume, 599326.363767, mm^3# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1050908.034545, mm^3# Measure IntraCranialVol, ICV, Intracranial Volume, 1734351.873615, mm^3# SegVolFile mri/aseg.mgz* and *Title Segmentation Statistics # # generating_program mri_segstats# cvs_version $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $# cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject PRI018 # sysname Linux# hostname deckard.localdomain# machine x86_64# user fernanda.hansen# anatomy_type volume# # SUBJECTS_DIR /dados1/PROJETOS/PRJ1513_GIRIFICACAO_CONTROLES/03_PROCS/PREPROC_DATA/3DT1_ALZ_FOLLOWS# subjectname PRI018# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 939020.000000, mm^3# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 903909.000000, mm^3# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 903725.881149, mm^3# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 194350.327731, mm^3# Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 194703.516764, mm^3# Measure Cortex, CortexVol, Total cortical gray matter volume, 389053.844495, mm^3# Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left hemisphere cortical white matter volume, 182649.297520, mm^3# Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right hemisphere cortical white matter volume, 182762.739133, mm^3# Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical white matter volume, 365412.036654, mm^3# Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 52056.000000, mm^3# Measure TotalGray, TotalGrayVol, Total gray matter volume, 518287.844495, mm^3# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 839187.881149, mm^3# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 807827.881149, mm^3# Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, Supratentorial volume voxel count, 806671.000000, mm^3# Measure Mask, MaskVol, Mask Volume, 1368243.000000, mm^3# Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of BrainSegVol to eTIV, 0.663000, unitless# Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, 0.966056, unitless# Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh surfaces prior to fixing, 62, unitless# Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh surfaces prior to fixing, 93, unitless# Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in surfaces prior to fixing, 155, unitless# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1416319.091398, mm^3# SegVolFile mri/aseg.mgz * How can I have the aseg.stats files all the same, with the SupraTentorialVolNotVent? Thank you in advance! -- Fernanda Hansen P. de Moraes Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz

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mri_vol2surf warning
by Rachel Bencic 02 May '18

02 May '18

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to resample beta weights generated from AFNI’s 3dDeconvolve command to individual subjects’ cortical surfaces. Prior to running 3dDeconvolve, I ran bbregister to coregister subjects’ (unwarped) functional data to their T1 anatomical scans and to generate a registration file to be used in the mri_vol2surf command. However, I get the following warning when I run the mri_vol2surf command: WARNING: the voxel resolution in the source volume (3.75, 3.75, 3.75) differs from that listed in the registration file (3.75, 3.75, 5) I've searched the list and came across a potentially similar case from Apr. 26, 2011 (SUBJECT: (no subject), AUTHOR: Kevin Bickart), which included the following advice: Hi Kevin, you can ignore that warning. The values in the registration file are not correct. doug I thought I would reach out to inquire as to whether this is still the case (i.e., that this warning can be ignored) or if it might be a more serious issue? I will add that mri_vol2surf did appear to run successfully (i.e., it did not error out) and provided a .mgh file as output. In case it is helpful, as a next step I plan to convert the .mgh file to an ASCII file to extract the time series. Ultimately, I plan to run graph analyses on the time series data. Any feedback you have would be greatly appreciated. Rachel 1) FreeSurfer version: freesurfer_6.0_x86_64 2) Platform: OSX High Sierra Here is my command: mri_vol2surf --mov ../betaEPI/ Betas_EPIpreproc.nii --srcreg ../bbregistration.dat --hemi lh --projfrac 0.5 --o ./lh.1.mgh mris_convert -c ./lh.1.mgh $parc_dir/${1}/surf/lh.white ../lh_ascii/lh.1.asc And the full output: srcvol = ../betaEPI/Betas_EPIpreproc.nii srcreg = ../bbregistration.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. Input reg is register.dat WARNING: the voxel resolution in the source volume (3.75,3.75,3.75) differs from that listed in the registration file (3.75,3.75,5) -------- original matrix ----------- 0.99988 -0.00997 0.01155 -0.43638; -0.01472 -0.43023 0.90260 22.14351; 0.00403 0.90266 0.43033 34.58801; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Reading surface /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/lh.white Done reading source surface Reading thickness /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 8657 Writing to ./lh.1.mgh Dim: 146930 1 1 srcvol = ../betaEPI/Betas_EPIpreproc.nii srcreg = ../bbregistration.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. Input reg is register.dat WARNING: the voxel resolution in the source volume (3.75,3.75,3.75) differs from that listed in the registration file (3.75,3.75,5) -------- original matrix ----------- 0.99988 -0.00997 0.01155 -0.43638; -0.01472 -0.43023 0.90260 22.14351; 0.00403 0.90266 0.43033 34.58801; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Reading surface /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/rh.white Done reading source surface Reading thickness /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 8681 Writing to ./rh.1.mgh Dim: 148618 1 1

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Re: [Freesurfer] problem using mri_vol2label for subcortical regions
by Lucia Billeci 02 May '18

02 May '18

External Email - Use Caution Dear Brouce, thanks again. I would like exactly how to set mri_vol2label for subcortical regions as the way I used give me all the values of the first column equal to -1. This is a problem when I want to obtain obtain the centroid of the ROI using mri_surfcluster as I get an empty file. Hope Doug can help me. Thanks Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa, Italy e-mail: lucia.billeci(a)ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > On 2 May 2018, at 16:01, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > Hi Lucia > > can you cc the list so others can answer? You can't get a surface-based label for a subcortical region as they aren't on (or close) to the surrface. I think mri_vol2label is the right binary to create a volumetric ROI for each one, but Doug will know > cheers > Bruce > > On Wed, 2 May 2018, Lucia Billeci wrote: > >> External Email - Use Caution >> Dear Bruce, >> thanks for your answer. >> I would like to obtain .label file for each subcortical region. I have tried the commands I >> reported in the previous messages but probably they are not correct. Could you please indicate me >> the correct way to have the .label file for subcortical regions? I am not sure if >> using mri_vol2label is the right way or maybe there is another strategy. >> Thanks >> regards >> Lucia >> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >> Dr. Lucia Billeci, PhD >> Institute of Clinical Physiology (IFC) National Research Council (CNR) >> via Moruzzi 1, 56124, Pisa, Italy >> e-mail: lucia.billeci(a)ifc.cnr.it >> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail.

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kvlGEMSMatlab error: search direction is not a descent direction
by Wayne Su 02 May '18

02 May '18

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run longitudinal segmentation of hippocampal subfields by using the development version of FreeSurfer, but for some of my subjects I get the following error: ******************* Global iteration 3 ******************* ***** Estimating subject-specific atlas ***** L-BFGS Verbose: 0 MaximalDeformationStopCriterion: 1e-10 LineSearchMaximalDeformationIntervalStopCriterion: 1e-10 MaximumNumberOfIterations: 1000 BFGS-MaximumMemoryLength: 12 Subject atlas deformation, step 1 of 400 Did one deformation step of max. 0.38685 voxels in 7.733 seconds minLogLikelihoodTimesPrior = 1.0297e+05 Subject atlas deformation, step 2 of 400 Error using kvlGEMSMatlab /autofs/space/panamint_005/users/iglesias/software/freesurfer/GEMS2/kvlAtlas MeshDeformationOptimizer.cxx:327: itk::ERROR: AtlasMeshDeformationLBFGSOptimizer(0x2b53b9427df0): search direction is not a descent direction! Error in kvlStepOptimizer (line 11) Error in SegmentSubfieldsT1Longitudinal (line 1169) Does anyone have any thoughts on how to trouble-shoot this one? Also, I¹ve attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-x86_64-unknown-linux-gnu-dev-20180426 2) Platform: CentOS Linux release 7.4.1708 (Core) 3) uname -a: Linux bcmhari-hpc12 3.10.0-327.el7.x86_64 #1 SMP Thu Nov 19 22:10:57 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thanks, Wayne

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aseg labels in nii | FreeSurfer to other software
by Otília 02 May '18

02 May '18

External Email - Use Caution Hi to all FS users! Sorry in advance if I'm _cross-posting_ but after searching and trying some stuff I still can't figure out how to do this. After all the processing in FS I would like to evaluate the labels (from each participant) in other software (aseg labels). I imagine I would need to binarize the label of each subject as masks or volumes, in .nii or some more common file type. Do someone know how to do that? Any help would be very much appreciated! Thank you! Best regards, Otília

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Freesurfer May 2018