Re: [Freesurfer] fcseed-sess error
Hi Doug, It is a pretty small segmentation. In subject NNC0931 (the example we're looking at) the segmentation has 54 voxels. fcseed-sess also didn't work in subject NNC0901 -- in that subject the segmentation has 78 voxels. For comparison, in one of the subjects where fcseed-sess completed without error the segmentation has 89 voxels. Do you think this is an issue of size? Thanks! Alex I'm not sure what is going wrong here, but it does not find any voxels when the segmentation is mapped into the functional space. Can you look at /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz And see how many voxels it has? Is it possible that that is a really small segmentation? doug On 05/21/2015 10:30 AM, Alexandra Tanner wrote: Hi Doug and Freesurfers, I'm running fcseed-sess to compute the time course in 12 different ROIs (created with fcseed-config) across 27 subjects. I'm having an issue, however, where fcseed-sess completes for a particular ROI in most subjects but errors out for a few subjects (see log below). I saw someone had the same issue in the mail archives (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-August/032646.html) so I checked the registration but everything seems to look fine. Any other suggestions on how to fix this issue would be greatly appreciated! Thanks! Alex fcseed-config and fcseed-sess commands/logs: # /usr/local/freesurfer/dev/fsfast/bin/fcseed-config -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg -segid 1 -seg lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz -fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat -fsd resting -mean -force # ProjectDir /autofs/cluster/roffman/users/Stable5_PerRun # $Id: fcseed-config,v 1.8 2014/02/25 19:08:31 greve Exp $ # Wed May 20 14:03:50 EDT 2015 fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat fsd resting segstem lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol RegDOF 6 FillThresh .5 DoMean 1 DoSVD 0 DoSqr 0 MakeMask 0 WMErode 0 SVDSynth 0 DoWM 0 UseB0DC 0 segidlist 1 Tue May 19 17:40:27 EDT 2015 Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/dev/fsfast/bin/fcseed-sess -s NNC0931 -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg freesurfer-Linux-centos6_x86_64-dev-20150519 mri_label2vol --seg /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz --reg /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta --temp /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii --fillthresh .5 --o /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii --pvf /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii PVF /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii Number of labels: 0 Annot File: (null) Template Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii Outut Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii Registration File: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ Template RAS-to-Vox: -0.3 -0.0 -0.0 36.0; -0.0 -0.0 -0.3 36.0; -0.0 0.3 -0.0 23.5; -0.0 -0.0 -0.0 1.0; Template Voxel Volume: 27 nHits Thresh: 13.5 Loading registration from /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta regio_read_register: loading lta RegMat: 0.99848 0.02007 -0.05128 -0.41633; 0.04918 0.09388 0.99437 -30.67201; -0.02477 0.99538 -0.09275 5.35657; 0.0 0.0 0.0 1.0; Label RAS-to-Vox: -0.33283 -0.00669 0.01709 36.13877; 0.00826 -0.33179 0.03092 34.21448; 0.01639 0.03129 0.33146 13.27600; 0.0 0.0 0.0 1.0; PVF /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii Computing PVF 27
[Freesurfer] fcseed-sess error
Hi Doug and Freesurfers, I'm running fcseed-sess to compute the time course in 12 different ROIs (created with fcseed-config) across 27 subjects. I'm having an issue, however, where fcseed-sess completes for a particular ROI in most subjects but errors out for a few subjects (see log below). I saw someone had the same issue in the mail archives (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-August/032646.html) so I checked the registration but everything seems to look fine. Any other suggestions on how to fix this issue would be greatly appreciated! Thanks! Alex fcseed-config and fcseed-sess commands/logs: # /usr/local/freesurfer/dev/fsfast/bin/fcseed-config -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg -segid 1 -seg lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz -fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat -fsd resting -mean -force # ProjectDir /autofs/cluster/roffman/users/Stable5_PerRun # $Id: fcseed-config,v 1.8 2014/02/25 19:08:31 greve Exp $ # Wed May 20 14:03:50 EDT 2015 fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat fsd resting segstem lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol RegDOF 6 FillThresh .5 DoMean 1 DoSVD 0 DoSqr 0 MakeMask 0 WMErode 0 SVDSynth 0 DoWM 0 UseB0DC 0 segidlist 1 Tue May 19 17:40:27 EDT 2015 Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/dev/fsfast/bin/fcseed-sess -s NNC0931 -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg freesurfer-Linux-centos6_x86_64-dev-20150519 mri_label2vol --seg /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz --reg /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta --temp /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii --fillthresh .5 --o /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii --pvf /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii PVF /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii Number of labels: 0 Annot File: (null) Template Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii Outut Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii Registration File: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ Template RAS-to-Vox: -0.3 -0.0 -0.0 36.0; -0.0 -0.0 -0.3 36.0; -0.0 0.3 -0.0 23.5; -0.0 -0.0 -0.0 1.0; Template Voxel Volume: 27 nHits Thresh: 13.5 Loading registration from /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta regio_read_register: loading lta RegMat: 0.99848 0.02007 -0.05128 -0.41633; 0.04918 0.09388 0.99437 -30.67201; -0.02477 0.99538 -0.09275 5.35657; 0.0 0.0 0.0 1.0; Label RAS-to-Vox: -0.33283 -0.00669 0.01709 36.13877; 0.00826 -0.33179 0.03092 34.21448; 0.01639 0.03129 0.33146 13.27600; 0.0 0.0 0.0 1.0; PVF /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii Computing PVF 27 mri_label2vol done mri_binarize --i /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii --o /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/mask.nii --match 1 $Id: mri_binarize.c,v 1.41 2014/08/17 17:47:29 greve Exp $ cwd /autofs/cluster/roffman/users/Stable5_PerRun cmdline mri_binarize --i /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii --o /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/mask.nii --match 1 sysname Linux hostname dauntless machine x86_64 user atanner input /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii frame 0 nErode3d 0 nErode2d 0 output /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/mask.nii
Re: [Freesurfer] fcseed-sess error
The voxel size for this functional sequence is 3x3x3mm What is the voxel size of your functional? 54 is small, but I would expect it to still work. On 05/21/2015 11:20 AM, Alexandra Tanner wrote: Hi Doug, It is a pretty small segmentation. In subject NNC0931 (the example we're looking at) the segmentation has 54 voxels. fcseed-sess also didn't work in subject NNC0901 -- in that subject the segmentation has 78 voxels. For comparison, in one of the subjects where fcseed-sess completed without error the segmentation has 89 voxels. Do you think this is an issue of size? Thanks! Alex I'm not sure what is going wrong here, but it does not find any voxels when the segmentation is mapped into the functional space. Can you look at /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz And see how many voxels it has? Is it possible that that is a really small segmentation? doug On 05/21/2015 10:30 AM, Alexandra Tanner wrote: Hi Doug and Freesurfers, I'm running fcseed-sess to compute the time course in 12 different ROIs (created with fcseed-config) across 27 subjects. I'm having an issue, however, where fcseed-sess completes for a particular ROI in most subjects but errors out for a few subjects (see log below). I saw someone had the same issue in the mail archives (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-August/032646.html) so I checked the registration but everything seems to look fine. Any other suggestions on how to fix this issue would be greatly appreciated! Thanks! Alex fcseed-config and fcseed-sess commands/logs: # /usr/local/freesurfer/dev/fsfast/bin/fcseed-config -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg -segid 1 -seg lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz -fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat -fsd resting -mean -force # ProjectDir /autofs/cluster/roffman/users/Stable5_PerRun # $Id: fcseed-config,v 1.8 2014/02/25 19:08:31 greve Exp $ # Wed May 20 14:03:50 EDT 2015 fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat fsd resting segstem lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol RegDOF 6 FillThresh .5 DoMean 1 DoSVD 0 DoSqr 0 MakeMask 0 WMErode 0 SVDSynth 0 DoWM 0 UseB0DC 0 segidlist 1 Tue May 19 17:40:27 EDT 2015 Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/dev/fsfast/bin/fcseed-sess -s NNC0931 -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg freesurfer-Linux-centos6_x86_64-dev-20150519 mri_label2vol --seg /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz --reg /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta --temp /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii --fillthresh .5 --o /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii --pvf /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii PVF /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii Number of labels: 0 Annot File: (null) Template Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii Outut Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii Registration File: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ Template RAS-to-Vox: -0.3 -0.0 -0.0 36.0; -0.0 -0.0 -0.3 36.0; -0.0 0.3 -0.0 23.5; -0.0 -0.0 -0.0 1.0; Template Voxel Volume: 27 nHits Thresh: 13.5 Loading registration from /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta regio_read_register: loading lta RegMat: 0.99848 0.02007 -0.05128 -0.41633; 0.04918 0.09388 0.99437 -30.67201; -0.02477 0.99538 -0.09275 5.35657; 0.0 0.0 0.0 1.0; Label RAS-to-Vox: -0.33283 -0.00669 0.01709 36.13877
Re: [Freesurfer] fcseed-sess error
I actually already tried rerunning fcseed-config and fcseed-sess lowering the fillthresh (even brought it down to 0) and I still got the same error. I just tried .05 to be thorough but no dice :( Try lowering the fillthreshold to .1 in fcseed-config (means you have to re-run fcseed-sess for all subjects, but see if it makes those two work). For such a small seed, it may even be better to use .05. On 05/21/2015 11:42 AM, Alexandra Tanner wrote: The voxel size for this functional sequence is 3x3x3mm What is the voxel size of your functional? 54 is small, but I would expect it to still work. On 05/21/2015 11:20 AM, Alexandra Tanner wrote: Hi Doug, It is a pretty small segmentation. In subject NNC0931 (the example we're looking at) the segmentation has 54 voxels. fcseed-sess also didn't work in subject NNC0901 -- in that subject the segmentation has 78 voxels. For comparison, in one of the subjects where fcseed-sess completed without error the segmentation has 89 voxels. Do you think this is an issue of size? Thanks! Alex I'm not sure what is going wrong here, but it does not find any voxels when the segmentation is mapped into the functional space. Can you look at /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz And see how many voxels it has? Is it possible that that is a really small segmentation? doug On 05/21/2015 10:30 AM, Alexandra Tanner wrote: Hi Doug and Freesurfers, I'm running fcseed-sess to compute the time course in 12 different ROIs (created with fcseed-config) across 27 subjects. I'm having an issue, however, where fcseed-sess completes for a particular ROI in most subjects but errors out for a few subjects (see log below). I saw someone had the same issue in the mail archives (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-August/032646.html) so I checked the registration but everything seems to look fine. Any other suggestions on how to fix this issue would be greatly appreciated! Thanks! Alex fcseed-config and fcseed-sess commands/logs: # /usr/local/freesurfer/dev/fsfast/bin/fcseed-config -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg -segid 1 -seg lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz -fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat -fsd resting -mean -force # ProjectDir /autofs/cluster/roffman/users/Stable5_PerRun # $Id: fcseed-config,v 1.8 2014/02/25 19:08:31 greve Exp $ # Wed May 20 14:03:50 EDT 2015 fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat fsd resting segstem lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol RegDOF 6 FillThresh .5 DoMean 1 DoSVD 0 DoSqr 0 MakeMask 0 WMErode 0 SVDSynth 0 DoWM 0 UseB0DC 0 segidlist 1 Tue May 19 17:40:27 EDT 2015 Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/dev/fsfast/bin/fcseed-sess -s NNC0931 -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg freesurfer-Linux-centos6_x86_64-dev-20150519 mri_label2vol --seg /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz --reg /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta --temp /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii --fillthresh .5 --o /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii --pvf /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii PVF /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii Number of labels: 0 Annot File: (null) Template Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii Outut Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii Registration File: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ Template RAS-to-Vox: -0.3 -0.0 -0.0 36.0; -0.0 -0.0 -0.3 36.0; -0.0 0.3 -0.0 23.5; -0.0 -0.0 -0.0 1.0
Re: [Freesurfer] fcseed-sess error
Hi Doug, So I just tried making my ROI a little bit bigger in an earlier binarizing step that created my segmentation, and when I ran fcseed-config and fcseed-sess in this same subject it ran without error. I guess it was a sizing issue! Let me know if you have any additional thoughts. Thanks again for your help! Best, Alex I actually already tried rerunning fcseed-config and fcseed-sess lowering the fillthresh (even brought it down to 0) and I still got the same error. I just tried .05 to be thorough but no dice :( Try lowering the fillthreshold to .1 in fcseed-config (means you have to re-run fcseed-sess for all subjects, but see if it makes those two work). For such a small seed, it may even be better to use .05. On 05/21/2015 11:42 AM, Alexandra Tanner wrote: The voxel size for this functional sequence is 3x3x3mm What is the voxel size of your functional? 54 is small, but I would expect it to still work. On 05/21/2015 11:20 AM, Alexandra Tanner wrote: Hi Doug, It is a pretty small segmentation. In subject NNC0931 (the example we're looking at) the segmentation has 54 voxels. fcseed-sess also didn't work in subject NNC0901 -- in that subject the segmentation has 78 voxels. For comparison, in one of the subjects where fcseed-sess completed without error the segmentation has 89 voxels. Do you think this is an issue of size? Thanks! Alex I'm not sure what is going wrong here, but it does not find any voxels when the segmentation is mapped into the functional space. Can you look at /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz And see how many voxels it has? Is it possible that that is a really small segmentation? doug On 05/21/2015 10:30 AM, Alexandra Tanner wrote: Hi Doug and Freesurfers, I'm running fcseed-sess to compute the time course in 12 different ROIs (created with fcseed-config) across 27 subjects. I'm having an issue, however, where fcseed-sess completes for a particular ROI in most subjects but errors out for a few subjects (see log below). I saw someone had the same issue in the mail archives (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-August/032646.html) so I checked the registration but everything seems to look fine. Any other suggestions on how to fix this issue would be greatly appreciated! Thanks! Alex fcseed-config and fcseed-sess commands/logs: # /usr/local/freesurfer/dev/fsfast/bin/fcseed-config -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg -segid 1 -seg lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz -fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat -fsd resting -mean -force # ProjectDir /autofs/cluster/roffman/users/Stable5_PerRun # $Id: fcseed-config,v 1.8 2014/02/25 19:08:31 greve Exp $ # Wed May 20 14:03:50 EDT 2015 fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat fsd resting segstem lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol RegDOF 6 FillThresh .5 DoMean 1 DoSVD 0 DoSqr 0 MakeMask 0 WMErode 0 SVDSynth 0 DoWM 0 UseB0DC 0 segidlist 1 Tue May 19 17:40:27 EDT 2015 Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/dev/fsfast/bin/fcseed-sess -s NNC0931 -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg freesurfer-Linux-centos6_x86_64-dev-20150519 mri_label2vol --seg /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz --reg /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta --temp /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii --fillthresh .5 --o /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii --pvf /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii PVF /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii Number of labels: 0 Annot File: (null) Template Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii Outut Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii Registration File: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv
[Freesurfer] Talairach coordinate discrepancy mri_surfcluster vs tksurfer
Hi Doug and Freesurfers, I ran mri_surfcluster to generate coordinates for cluster maxima from a functional surface analysis. The summary text file generated by mri_surfcluster lists a bunch of information about the clusters, including talairach coordinates for each cluster peak (see example below). I visualized these max vertices in tksurfer by entering the VtxMax given in the summary file into the Vertex Index field in the tksurfer tools window. I'm noticing, however, that the talairach coordinates given in the tksurfer tools window (Vertex Talairach) after entering the vertex index are not the same as the coordinates listed in the summary file. Seems the coordinates are off by .5 - 1 millimeter or so, which I know is not much, but I'm curious if anyone knows the reason for this discrepancy? Additionally, if we want to use the peaks for seeds in a functional connectivity analysis which set of coordinates is more accurate? Any insight would be greatly appreciated! Best, Alex Ex. Summary text file: # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZNVtxs 1 33.019 124877 1219.98 30.7 21.1 -1.4 2841 2 27.538 116676 1406.49 7.6 23.7 38.1 2923 3 25.380 109387 3977.58 41.9 31.2 26.7 7023 4 24.404 86863 3241.21 31.5 -60.2 39.0 7288 5 -20.441 104109 1903.13 5.5 20.5 -7.4 3923 6 18.118 141781600.75 5.5 -23.0 26.4 1553 Cluster 1 Vertex Talairach coordinates from tksurfer tools: (29.88 20.79 -1.32) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] [Fwd: Re: Modeling cortical thickness question]
Hi Doug, Thanks for your response! Please see Josh's follow-up question below. Thanks again for your help! Best, Alex Original Message Subject: Re: [Fwd: Re: [Freesurfer] Modeling cortical thickness question] From:Roffman, Joshua L.,M.D. jroff...@partners.org Date:Wed, December 10, 2014 11:52 am To: Alexandra Tanner atan...@nmr.mgh.harvard.edu -- Maybe...if we take this approach I guess we would want the cube root of age, not age cubed? The relationship we are testing is whether y=x^3 (where x is age and y is cortical thickness). So if we took the cube root of both sides, that might be closer to what we want? (Alex: could you forward this to the list) Thx Josh Sent from my iPhone On Dec 10, 2014, at 9:32 AM, Alexandra Tanner atan...@nmr.mgh.harvard.edu wrote: Hi Josh, Below is Doug's response...does this answer your question? Thanks, Alex Original Message Subject: Re: [Freesurfer] Modeling cortical thickness question From:Douglas N Greve gr...@nmr.mgh.harvard.edu Date:Tue, December 9, 2014 4:48 pm To: freesurfer@nmr.mgh.harvard.edu -- Do you mean a polynomial of age? If so, just add age age^2 and age^3 as variables in the FSGD file doug On 12/09/2014 02:04 PM, Alexandra Tanner wrote: Hello Freesurfers, Our group is wondering if any of you know whether it is possible to model cortical thickness as a third order polynomial? The specific question is: we are looking at whether there is a hyperbolic relationship between cortical thickness and date of birth among a cohort of individuals born over a 6 year period. Any insights would be greatly appreciated! Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Modeling cortical thickness question
Hello Freesurfers, Our group is wondering if any of you know whether it is possible to model cortical thickness as a third order polynomial? The specific question is: we are looking at whether there is a hyperbolic relationship between cortical thickness and date of birth among a cohort of individuals born over a 6 year period. Any insights would be greatly appreciated! Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] funcroi calculating percent signal change
Hi Doug, Thanks, this seems to work! Quick question -- in the past we've done ROI analyses where we've functionally constrained our labels. When calculating percent signal change we would take the output from funcroi-table-sess divide it by the output of funcroi-table-sess with no -c flag (the baseline offset value) and multiply by 100. Is this also a correct method for calculating percent signal change? I've tried it for the current ROI I'm using and compared my calculated value to the value I got by adding -m cespct and the numbers I'm getting are not the same (ex. 0.0159 vs 0.01444 for one subject). Is -m cespct more accurate? Thanks! Best, Alex Hi Alex, if you use -m cespct it will report the mean percent signal change within the ROI. Does this work? doug On 10/31/2013 02:37 PM, Alexandra Tanner wrote: Hi Doug and Freesurfers, I would like to calculate percent signal change within an anatomical ROI for a group of subjects in Freesurfer 5.0. We are not functionally constraining our ROI, however, we do want to calculate the percent signal change across the entire region in each of our conditions (the contrasts we are using are condition-vs-fixation). Below are examples of the commands I've run for one of our conditions: funcroi-config -analysis SIRP_Stable5 -label lh.7Network_6.PFC.label -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg funcroi-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED funcroi-table-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED -o /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/18ActiveFolate_12Placebo_PreAndPost_7Tpost/lh_7Networks_6_PFC_1vFix -c Cond1vFix Is it necessary to now generate the mean functional baseline offset value within the ROI in order to calculate percent signal change if our contrast is comparing condition-vs-fixation? Any clarification on when the offset value is needed would be greatly appreciated! Thanks, Alex -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] funcroi calculating percent signal change
Great, thanks for the clarification Doug! Best, Alex It depends on how are you defining percent contrast. What you are are slightly different methods. Using -m cespct is equivalent to computing 100*Sum(contrast_i/baseline_i)/N where i is a voxel in the ROI Your method is equivalent to computing 100*Sum(contrast_i)/Sum(baseline_i) So they will be close but not exact. Which one is better? Hard to say. I would tend toward -m cespect doug On 11/01/2013 01:43 PM, Alexandra Tanner wrote: Hi Doug, Thanks, this seems to work! Quick question -- in the past we've done ROI analyses where we've functionally constrained our labels. When calculating percent signal change we would take the output from funcroi-table-sess divide it by the output of funcroi-table-sess with no -c flag (the baseline offset value) and multiply by 100. Is this also a correct method for calculating percent signal change? I've tried it for the current ROI I'm using and compared my calculated value to the value I got by adding -m cespct and the numbers I'm getting are not the same (ex. 0.0159 vs 0.01444 for one subject). Is -m cespct more accurate? Thanks! Best, Alex Hi Alex, if you use -m cespct it will report the mean percent signal change within the ROI. Does this work? doug On 10/31/2013 02:37 PM, Alexandra Tanner wrote: Hi Doug and Freesurfers, I would like to calculate percent signal change within an anatomical ROI for a group of subjects in Freesurfer 5.0. We are not functionally constraining our ROI, however, we do want to calculate the percent signal change across the entire region in each of our conditions (the contrasts we are using are condition-vs-fixation). Below are examples of the commands I've run for one of our conditions: funcroi-config -analysis SIRP_Stable5 -label lh.7Network_6.PFC.label -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg funcroi-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED funcroi-table-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED -o /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/18ActiveFolate_12Placebo_PreAndPost_7Tpost/lh_7Networks_6_PFC_1vFix -c Cond1vFix Is it necessary to now generate the mean functional baseline offset value within the ROI in order to calculate percent signal change if our contrast is comparing condition-vs-fixation? Any clarification on when the offset value is needed would be greatly appreciated! Thanks, Alex -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] funcroi calculating percent signal change
Hi Doug and Freesurfers, I would like to calculate percent signal change within an anatomical ROI for a group of subjects in Freesurfer 5.0. We are not functionally constraining our ROI, however, we do want to calculate the percent signal change across the entire region in each of our conditions (the contrasts we are using are condition-vs-fixation). Below are examples of the commands I've run for one of our conditions: funcroi-config -analysis SIRP_Stable5 -label lh.7Network_6.PFC.label -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg funcroi-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED funcroi-table-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED -o /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/18ActiveFolate_12Placebo_PreAndPost_7Tpost/lh_7Networks_6_PFC_1vFix -c Cond1vFix Is it necessary to now generate the mean functional baseline offset value within the ROI in order to calculate percent signal change if our contrast is comparing condition-vs-fixation? Any clarification on when the offset value is needed would be greatly appreciated! Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Make an average activation map of 2 scans
Hi Freesurfers, Does anyone know how to make an average activation map of two subjects without running a group analysis? I have 15 subjects that each have a pre and a post scan (30 scans total) and we would like to combine the pre and post bold runs for each subject to generate an averaged AllvFix activation map for each pair (so I would end up with 1 activation map per subject pair of the pre and post bold runs averaged together -- 15 maps total). Originally I tried treating each of my subject pairs as a group and ran isxconcat-sess and mri_glmfit on each pair (N=2), but because my N was so small the osgm map looked very strange and wispy. Because I'm trying to combine a pre and post scan for the same subject, is it possible to register the post subject's bold scans to the pre subject (or vice versa) so that we can treat all the bold runs as one subject and run selxavg3-sess referencing the pre and post bold runs in the runlist file? Any clarification or suggestions would be greatly appreciated! Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] funcroi-table-sess error
Hi Doug, I was running the command out of the $SUBJECTS_DIR. I created a log folder in the $SUBJECTS_DIR and then the command ran smoothly! Thanks! Best, Alex Hi Alex, are you running it from the project folder? It is looking for a folder called log in the current directory. It should be creating this folder (bug). So, if you run it from the project folder, the log folder will be there. Or can create a log folder in your current directory (mkdir log) doug On 7/30/13 2:03 PM, Alexandra Tanner wrote: Dear Doug and Freesurfers, I am attempting to run funcroi-table-sess on a set of subjects but keep getting an error message I've never seen before: funcroi-table-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/ctx.lh.insula.aparc+aseg_2vFix.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED -c Cond2vFix -o /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/18ActiveFolate_12Placebo_PreAndPost_7Tpost/ctx_lh_insula_aparc+aseg_2vFix log/funcroi-table-sess.log log/funcroi-table-sess.log: No such file or directory. Funcroi-sess ran without error, as did funcroi-config. I've run this analysis many times in the past and have never had this problem so I am at a loss as to what is going wrong. Any help would be greatly appreciated! Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] funcroi-table-sess error
Dear Doug and Freesurfers, I am attempting to run funcroi-table-sess on a set of subjects but keep getting an error message I've never seen before: funcroi-table-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/ctx.lh.insula.aparc+aseg_2vFix.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED -c Cond2vFix -o /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/18ActiveFolate_12Placebo_PreAndPost_7Tpost/ctx_lh_insula_aparc+aseg_2vFix log/funcroi-table-sess.log log/funcroi-table-sess.log: No such file or directory. Funcroi-sess ran without error, as did funcroi-config. I've run this analysis many times in the past and have never had this problem so I am at a loss as to what is going wrong. Any help would be greatly appreciated! Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Contrast file for cortical thickness 2 group 1 covariate analysis
Hi Doug, I apologize if my last email was a bit confusing/lacking in information. Dr. Roffman gives a more thorough explanation of what we're trying to achieve (see below). Hopefully this gives you a better idea of what we're asking -- thanks! We are looking at the relationship between age and cortical thickness in two independent groups (each n=22). We are not interested in mapping the difference in slopes for the age-thickness relationship between group 1 and group 2. Rather, we are interested in mapping the significance of the difference in the age-thickness correlation strength between group 1 and group 2. Two distributions can have a similar slope, but the R2 for one group can be very different than the R2 for the other group, based on how tightly the datapoints conform to the best fit line for each group. That appears to be the case for our data. If we are using an ROI approach, we see that in group 1, within the left inferior frontal gyrus, when we look at Pearson's r for the relationship between cortical thickness and age, we get r=.717 (p=.0002). In group 2, within the same region, Pearson's r=.169 (p=.452). We can test for a difference in correlation strength between two groups by performing a Fisher r-to-z transformation. With 22 subjects in each group, this yields a z score of 2.25, and p=.0244, indicating that the correlation is significantly stronger in group 1 than in group 2. The question is whether we can apply this approach in a vertex-wise manner and see where across the brain there are differences in age-thickness correlation strength between the two groups. Any advice would be greatly appreciated! Best, Alex Hi Alex, I'm not sure I understand what you mean. What is the strength of the thickness/age relationship if not the slope between thickness and age? doug On 04/05/2013 03:56 PM, Alexandra Tanner wrote: Dear Doug and Freesurfers, I'm running a group cortical thickness analysis covaried by age, and we're curious if there is a way to correlate thickness and age within groups and then look at whether or not there is a difference in the strength of the thickness/age relationship between groups. Originally the contrast file we used was the group-x-age.mtx (0 0 1 -1) looking at whether or not there was a difference between the group age slopes, but we then realized we're not interested in whether the slopes of the relationships are different, but rather if the strength of the cortical thickness/age relationship differs between groups. I ran mri_glmfit with an fsgd file that was set up as follows: GroupDescriptorFile 1 Title OSGM Class Group1 Class Group2 Variables Age Input subject1 Group1 30 Input subject2 Group2 40 I've taken a look at the wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V) and can't seem to find a contrast file that does what we're looking for. Any advice on what sort of contrast file we should use, or whether we need to run a different analysis than glmfit, would be greatly appreciated! Thanks! Best, Alex -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Contrast file for cortical thickness 2 group 1 covariate analysis
Dear Doug and Freesurfers, I'm running a group cortical thickness analysis covaried by age, and we're curious if there is a way to correlate thickness and age within groups and then look at whether or not there is a difference in the strength of the thickness/age relationship between groups. Originally the contrast file we used was the group-x-age.mtx (0 0 1 -1) looking at whether or not there was a difference between the group age slopes, but we then realized we're not interested in whether the slopes of the relationships are different, but rather if the strength of the cortical thickness/age relationship differs between groups. I ran mri_glmfit with an fsgd file that was set up as follows: GroupDescriptorFile 1 Title OSGM Class Group1 Class Group2 Variables Age Input subject1 Group1 30 Input subject2 Group2 40 I've taken a look at the wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V) and can't seem to find a contrast file that does what we're looking for. Any advice on what sort of contrast file we should use, or whether we need to run a different analysis than glmfit, would be greatly appreciated! Thanks! Best, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] mergecontrasts-sess group map
Hi Doug, So if I run a group analysis with each contrast separately, would I then be running mri_concat to do a conjunction of the group sig maps? Also, can I merge more than 2 contrasts at once when using mri_concat? Thanks! Alex Hi Alex, unfortunately, you cannot compute a conjunction with the CES. That's the problem with trying to do group-wise multi-variate analysis. Another thing you can do is to do a group analysis with each contrast separately, then do a conjunction of the group sig maps. doug On 11/29/2012 03:39 PM, Alexandra Tanner wrote: Thanks for the clarification! So I will rerun mergecontrasts-sess using the ces image on my subjects and then run mri_vol2surf and mri_concat to get the group map. Thanks for your help! Best, Alex Usually the contrast effects size (ces) (in SPM this is the CON image, in FSL it is the COPE image). Univariate maps are usually passed up to the group level (the conjunction done with mergecontrasts is multivariate). doug On 11/29/2012 01:05 PM, Alexandra Tanner wrote: Hi Doug, Thanks for the response! Just out of curiosity, what map is typically used for group analyses? Should I have used a map other than sig on the individual subject level as well? Thanks! Alex You'll have to run mri_vol2surf on each one separately to bring it into the fsaverage space, then mri_concat to stack all of the maps into one file. At that point you can compute a mean (also with mri_concat). Generally, one does not do group analysis on sig maps though. doug On 11/27/2012 05:08 PM, Alexandra Tanner wrote: Hi Doug and Freesurfers, I recently used mergecontrasts-sess to merge two contrasts of an analysis in 50 different subjects. The command ran on each subject individually and created a sig.nii and sig.ovpl file within a merged contrast folder for each subject. I'd now like to look at an average map of the merged contrasts across all 50 subjects. Does anyone know how to go about getting this average map for my group of 50 subjects? Command I ran to get the sig.nii/sig.ovpl file for each subject: mergecontrasts-sess -mergedcontrast Merge_7vFix_1vFix -conjunction andor -analysis SIRP_Stable5 -contrast Cond7vFix 3 pos 0 -contrast Cond1vFix 3 pos 0 -map sig -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/50_MTH_Subjects -df /cluster/roffman/users/Stable5_PerRun Any help would be greatly appreciated! Thanks, Alex -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] mergecontrasts-sess group map
Hi Doug, Thanks for the response! Just out of curiosity, what map is typically used for group analyses? Should I have used a map other than sig on the individual subject level as well? Thanks! Alex You'll have to run mri_vol2surf on each one separately to bring it into the fsaverage space, then mri_concat to stack all of the maps into one file. At that point you can compute a mean (also with mri_concat). Generally, one does not do group analysis on sig maps though. doug On 11/27/2012 05:08 PM, Alexandra Tanner wrote: Hi Doug and Freesurfers, I recently used mergecontrasts-sess to merge two contrasts of an analysis in 50 different subjects. The command ran on each subject individually and created a sig.nii and sig.ovpl file within a merged contrast folder for each subject. I'd now like to look at an average map of the merged contrasts across all 50 subjects. Does anyone know how to go about getting this average map for my group of 50 subjects? Command I ran to get the sig.nii/sig.ovpl file for each subject: mergecontrasts-sess -mergedcontrast Merge_7vFix_1vFix -conjunction andor -analysis SIRP_Stable5 -contrast Cond7vFix 3 pos 0 -contrast Cond1vFix 3 pos 0 -map sig -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/50_MTH_Subjects -df /cluster/roffman/users/Stable5_PerRun Any help would be greatly appreciated! Thanks, Alex -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] mergecontrasts-sess group map
Thanks for the clarification! So I will rerun mergecontrasts-sess using the ces image on my subjects and then run mri_vol2surf and mri_concat to get the group map. Thanks for your help! Best, Alex Usually the contrast effects size (ces) (in SPM this is the CON image, in FSL it is the COPE image). Univariate maps are usually passed up to the group level (the conjunction done with mergecontrasts is multivariate). doug On 11/29/2012 01:05 PM, Alexandra Tanner wrote: Hi Doug, Thanks for the response! Just out of curiosity, what map is typically used for group analyses? Should I have used a map other than sig on the individual subject level as well? Thanks! Alex You'll have to run mri_vol2surf on each one separately to bring it into the fsaverage space, then mri_concat to stack all of the maps into one file. At that point you can compute a mean (also with mri_concat). Generally, one does not do group analysis on sig maps though. doug On 11/27/2012 05:08 PM, Alexandra Tanner wrote: Hi Doug and Freesurfers, I recently used mergecontrasts-sess to merge two contrasts of an analysis in 50 different subjects. The command ran on each subject individually and created a sig.nii and sig.ovpl file within a merged contrast folder for each subject. I'd now like to look at an average map of the merged contrasts across all 50 subjects. Does anyone know how to go about getting this average map for my group of 50 subjects? Command I ran to get the sig.nii/sig.ovpl file for each subject: mergecontrasts-sess -mergedcontrast Merge_7vFix_1vFix -conjunction andor -analysis SIRP_Stable5 -contrast Cond7vFix 3 pos 0 -contrast Cond1vFix 3 pos 0 -map sig -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/50_MTH_Subjects -df /cluster/roffman/users/Stable5_PerRun Any help would be greatly appreciated! Thanks, Alex -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] mergecontrasts-sess group map
Hi Doug and Freesurfers, I recently used mergecontrasts-sess to merge two contrasts of an analysis in 50 different subjects. The command ran on each subject individually and created a sig.nii and sig.ovpl file within a merged contrast folder for each subject. I'd now like to look at an average map of the merged contrasts across all 50 subjects. Does anyone know how to go about getting this average map for my group of 50 subjects? Command I ran to get the sig.nii/sig.ovpl file for each subject: mergecontrasts-sess -mergedcontrast Merge_7vFix_1vFix -conjunction andor -analysis SIRP_Stable5 -contrast Cond7vFix 3 pos 0 -contrast Cond1vFix 3 pos 0 -map sig -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/50_MTH_Subjects -df /cluster/roffman/users/Stable5_PerRun Any help would be greatly appreciated! Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] mris_anatomical_stats on multiple subjects
Hi again, This is a follow-up question to my previous email -- the method I used may not be the most efficient or the correct way to extract cortical thickness from manually created ROIs. I'm unfamiliar with how to obtain thickness data from a label, so I'm not sure if what I did is correct or if first I must convert my label to volume or to an annotation file. If anyone knows a better or more accurate way to measure thickness from the ROI I'd really appreciate your advice! Best, Alex Hi Doug and Freesurfers, I'm currently working on extracting thickness measurements from an ROI I manually created. I created my ROI label in tksurfer and applied the label to each subject I'd like to extract thickness data from using mri_label2label. I then used the following command to generate a stats file, with the thickness measurement, from my label: mris_anatomical_stats -f something.stats -l something.label subjid ?h (http://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit). This generated a stats file that gave me the average thickness for my ROI in my subject. I was wondering if there is a way to run the same command, but on multiple subjects at once, so as not to have to run this command on each individual subject. Any suggestions would be greatly appreciated! Best, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] mris_anatomical_stats on multiple subjects
Hi Doug and Freesurfers, I'm currently working on extracting thickness measurements from an ROI I manually created. I created my ROI label in tksurfer and applied the label to each subject I'd like to extract thickness data from using mri_label2label. I then used the following command to generate a stats file, with the thickness measurement, from my label: mris_anatomical_stats -f something.stats -l something.label subjid ?h (http://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit). This generated a stats file that gave me the average thickness for my ROI in my subject. I was wondering if there is a way to run the same command, but on multiple subjects at once, so as not to have to run this command on each individual subject. Any suggestions would be greatly appreciated! Best, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Help removing marking from DICOM/.nii files
Hi Doug, Thanks for the quick reply! It seems the value of the writing is much higher than any value elsewhere in the image (over 4000). Instructions on how to replace this value with values of nearby voxels would be great -- hopefully that will allow us to run the autorecon1 command on it. Thanks, Alex Hi Alex, there's no way to erase it in a way that you can recover the underlying signal. I'm surprised that such small things are causing the talairach to crash. If the writing is always the same value and that value does not appear in other parts of the image, you might be able to replace the value with values of nearby voxels. Let me know if you need some instructions on this. doug On 08/22/2012 02:08 PM, Alexandra Tanner wrote: Hi Doug, I'm currently working with 4-6 year old clinical pediatric non-Siemens DICOM files that I'm unpacking and preprocessing in freesurfer. So far we've been able to unpack the DICOMS to .nii format and successfully begin the autorecon process for our first few subjects. We've noticed, when looking at the raw scans for some of our subjects, however, there is writing (probably information from the scan console) included in the images, and in some slices, slightly overlapping with the outer edge of the skull/brain. When attempting to run the autorecon1 on these scans, the command terminates during the talairach transform. We're thinking, since we don't have this issue with all of our subjects, the writing may be what is causing the problem. I'm wondering if you know of any way to remove the writing from the images (I tried seeing if I could erase the lettering in tkmedit but it seems it can't be erased manually). Attached is a screenshot of a coronal slice with the writing. Any suggestions would be greatly appreciated! Thanks, Alex -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Clinical DICOM files
Hi Doug, Thanks! Do you know what command line I should use with dcmunpack? I can't specify the run number since I don't currently have that information for my scan, only the DICOM files. Typically when we unpack our Siemens files we use the following command line: unpacksdcmdir -src source -targ target -run last MEMPRAGE scan MPRAGE COR blah -- for this scan should I be converting to mgh/mgz instead? Thanks, Alex dcmunpack will convert them to whatever file format you want (don't use COR though). doug On 08/20/2012 09:51 AM, Alexandra Tanner wrote: Thanks Bruce. I see that because these are not Siemens scans I need to use the command dcmunpack instead of unpacksdcmdir, however, if the DICOM files are already saved on our cluster do the files need to be unpacked or simply converted to COR format using mri_convert? Thanks! Best, Alex Hi Alex The dicoms should be enough Bruce On Aug 16, 2012, at 4:10 PM, Alexandra Tanner atan...@nmr.mgh.harvard.edu wrote: Dear Doug, We're getting T1 DICOM files from the Clinical PACS System (via mi2b2) and would like to pull them info the freesurfer stream to get cortical thickness. In order to run the standard unpacking commands, do we need any other files besides the DICOM files themselves? Of note, these scans were acquired on a variety of clinical scanners at MGH. Any suggestions you have would be greatly appreciated! Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Talairach transform error
Dear Doug, As I mentioned in a previous email, I'm currently working with T1 DICOM files from the Clinical PACS System that I'd like to pull into the freesurfer stream to get cortical thickness. I've unpacked the data, converting the DICOM files to mgz format, and successfully ran the first recon-all command: recon-all -i input -s subject -force. I then proceeded to run the recon-all -autorecon-all -s subject command on my subject, but the command terminated about 5 minutes in and I received the following error message: # #@# Talairach Failure Detection Mon Aug 20 13:53:21 EDT 2012 /autofs/cluster/roffman/users/Stable5_PerRun/Subject2/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) Linux compute-0-35 2.6.32-220.23.1.el6.x86_64 #1 SMP Mon Jun 18 18:58:52 BST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Subject2 exited with ERRORS at Mon Aug 20 13:53:21 EDT 2012 I tried viewing the talairach.xfm file in tkregister2, as I saw someone else who received the same error message was instructed to do, but no image would load (in the coronal and horizontal views the screen remained black and had one thin strip of grey in the center; the sagittal view brought up a blank white screen). We know that our data is intact because Dr. Roffman is able to view images of this subject on his computer using the mi2b2 software, so do you think it is possible that somewhere earlier, either in the recon or the dcmunpack stages, there was an error with the data that wasn't recognized until doing the talairach transformation? Also, something else I noticed when looking at our subject's data, the talairach.xfm and talairach.auto.xfm files are different, even though for all other subjects I've run recons on they are the same -- could this be a contributing factor? I'm unsure how to proceed with the unpacking since I'm currently unable to perform any edits to the talairach registration to try and fix the error, so any suggestions would be very helpful and greatly appreciated! Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Clinical DICOM files
Dear Doug, We're getting T1 DICOM files from the Clinical PACS System (via mi2b2) and would like to pull them info the freesurfer stream to get cortical thickness. In order to run the standard unpacking commands, do we need any other files besides the DICOM files themselves? Of note, these scans were acquired on a variety of clinical scanners at MGH. Any suggestions you have would be greatly appreciated! Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Talairach registration
Hi Doug, I'm currently looking into doing surface edits on past data and I heard someone mention that one should never scale the brain when editing the talairach registration. I was wondering if this was true, or if it's okay to scale the brain so long as you check the scaling in all 3 dimensions after doing so. Any input would be great! Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Talairach registration
Thanks Doug! What do you mean by registering to an individual? Is editing the talairach registration for each individual subject not the same thing? Thanks, Alex Hi Alex, it is fine to scale the brain for the tal registration. It is when registering to an individual that one must be very careful with scaling. doug On 08/10/2012 08:51 AM, Alexandra Tanner wrote: Hi Doug, I'm currently looking into doing surface edits on past data and I heard someone mention that one should never scale the brain when editing the talairach registration. I was wondering if this was true, or if it's okay to scale the brain so long as you check the scaling in all 3 dimensions after doing so. Any input would be great! Thanks, Alex -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Freesurfer Question
Hi Doug, Sorry for all the confusion, I misunderstood what we were looking for. Right now what we want is the volume measurement in each of the subcortical regions for each subject, which you suggested with the asegstats2table command. Thanks so much for your help! Alex Hi Alex, what do you mean by a thickness map of the subcortical region? The subcortical structure are usually characterized by simple volume measurements (eg, hippocampus has a volume of XXX mm3). There are tools out there to do voxel based morphometry. Is this what you mean? doug On 07/24/2012 03:02 PM, Alexandra Tanner wrote: Hi Doug, We don't want to do ROIs because we're trying to get a thickness map of the entire subcortical region of the brain. Prior to trying this, we ran a within subjects paired analysis that gave us thickness maps of cortical surface. We ran these commands to look at the thickness maps in each of our two groups: mris_preproc --target fsaverage1 --hemi lh --meas thickness --out /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/15_ActiveFolate_PreAndPostPAIRED_Structural/LH/lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/15_ActiveFolate_PreAndPostPAIRED_Structural.fsgd --paired-diff mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/15_ActiveFolate_PreAndPostPAIRED_Structural.fsgd --C /cluster/roffman/users/fsgd/Top_Minus_Bottom.mtx cd /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/15_ActiveFolate_PreAndPostPAIRED_Structural/LH mri_glmfit --glmdir lh.paired-diff.sm05 --y lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/15_ActiveFolate_PreAndPostPAIRED2_Structural.fsgd osgm (and then the same for our second group) And then we ran these commands to get a thickness map for the interaction between the two groups: mris_preproc --target fsaverage1 --hemi lh --meas thickness --out /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/22_ActiveFolateAndPlacebo_PreAndPostPAIRED_Structural/LH/lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/22_ActiveFolateAndPlacebo_PreAndPostPAIRED_Structural.fsgd paired-diff mri_surf2surf --s fsaverage1 --hemi lh --fwhm 5 --sval lh.paired-diff.thickness.mgh --tval lh.paired-diff.thickness.sm05.mgh mri_glmfit --glmdir lh.paired-diff.sm05 --y lh.paired-diff.thickness.sm05.mgh --fsgd /cluster/roffman/users/fsgd/22_ActiveFolateAndPlacebo_PreAndPostPAIRED2_Structural.fsgd --C /cluster/roffman/users/fsgd/Top_Minus_Bottom.mtx Basically what we're wondering is if there's a way to do the same type of paired within subjects analyses on the same data that will instead generate volume thickness maps of the subcortical brain. I hope this clarifies my question a bit better, and if anyone has any ideas that'd be great! Thanks, Alex Hi Alex, do you want to do it on an ROI basis? If so, you can use asegstats2table to create a table of your subjects at the two time points, then import this table into SPSS. Or you can run the table through mri_glmfit to do the paired-t analysis. doug On 07/24/2012 01:56 PM, Alexandra Tanner wrote: Hi Doug, Yes, sorry about that! I realized after I'd sent the email to you that I should've sent the email to the freesurfer list as well. We were hoping to look at volume in subcortical regions of the brain -- basal ganglia, hippocampus, amygdala, etc. Do know if there are commands to do the within subjects paired analysis this way? And if so, what they are? Thanks so much! Alex Hi Alexandra, what structure are you looking to analyze? Ie, the volume of what? The volume of cortex? doug ps. In the future, please post such questions to the freesurfer list as it gives others the opportunity to answer and to learn. thanks! On 07/23/2012 12:03 PM, Alexandra Tanner wrote: Hi Mr. Greve, My name is Alex Tanner, I'm the new CRC for Dr. Roffman in the Brain Genomics Lab. I had a question regarding conducting volume analyses. On the freesurfer wiki there are commands that show how to conduct Paired Analyses to look at average surface, and I was curious if it was possible to do a paired analysis looking at volume instead. Any information you have would be very helpful. Thanks so much! Best, Alexandra Tanner Clinical Research Coordinator Laboratory for Brain Genomics Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p) 617.643.3215 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop
Re: [Freesurfer] Freesurfer Question
Hi Doug, Yes, sorry about that! I realized after I'd sent the email to you that I should've sent the email to the freesurfer list as well. We were hoping to look at volume in subcortical regions of the brain -- basal ganglia, hippocampus, amygdala, etc. Do know if there are commands to do the within subjects paired analysis this way? And if so, what they are? Thanks so much! Alex Hi Alexandra, what structure are you looking to analyze? Ie, the volume of what? The volume of cortex? doug ps. In the future, please post such questions to the freesurfer list as it gives others the opportunity to answer and to learn. thanks! On 07/23/2012 12:03 PM, Alexandra Tanner wrote: Hi Mr. Greve, My name is Alex Tanner, I'm the new CRC for Dr. Roffman in the Brain Genomics Lab. I had a question regarding conducting volume analyses. On the freesurfer wiki there are commands that show how to conduct Paired Analyses to look at average surface, and I was curious if it was possible to do a paired analysis looking at volume instead. Any information you have would be very helpful. Thanks so much! Best, Alexandra Tanner Clinical Research Coordinator Laboratory for Brain Genomics Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p) 617.643.3215 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Freesurfer Question
Hi Doug, We don't want to do ROIs because we're trying to get a thickness map of the entire subcortical region of the brain. Prior to trying this, we ran a within subjects paired analysis that gave us thickness maps of cortical surface. We ran these commands to look at the thickness maps in each of our two groups: mris_preproc --target fsaverage1 --hemi lh --meas thickness --out /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/15_ActiveFolate_PreAndPostPAIRED_Structural/LH/lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/15_ActiveFolate_PreAndPostPAIRED_Structural.fsgd --paired-diff mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/15_ActiveFolate_PreAndPostPAIRED_Structural.fsgd --C /cluster/roffman/users/fsgd/Top_Minus_Bottom.mtx cd /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/15_ActiveFolate_PreAndPostPAIRED_Structural/LH mri_glmfit --glmdir lh.paired-diff.sm05 --y lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/15_ActiveFolate_PreAndPostPAIRED2_Structural.fsgd osgm (and then the same for our second group) And then we ran these commands to get a thickness map for the interaction between the two groups: mris_preproc --target fsaverage1 --hemi lh --meas thickness --out /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/22_ActiveFolateAndPlacebo_PreAndPostPAIRED_Structural/LH/lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/22_ActiveFolateAndPlacebo_PreAndPostPAIRED_Structural.fsgd paired-diff mri_surf2surf --s fsaverage1 --hemi lh --fwhm 5 --sval lh.paired-diff.thickness.mgh --tval lh.paired-diff.thickness.sm05.mgh mri_glmfit --glmdir lh.paired-diff.sm05 --y lh.paired-diff.thickness.sm05.mgh --fsgd /cluster/roffman/users/fsgd/22_ActiveFolateAndPlacebo_PreAndPostPAIRED2_Structural.fsgd --C /cluster/roffman/users/fsgd/Top_Minus_Bottom.mtx Basically what we're wondering is if there's a way to do the same type of paired within subjects analyses on the same data that will instead generate volume thickness maps of the subcortical brain. I hope this clarifies my question a bit better, and if anyone has any ideas that'd be great! Thanks, Alex Hi Alex, do you want to do it on an ROI basis? If so, you can use asegstats2table to create a table of your subjects at the two time points, then import this table into SPSS. Or you can run the table through mri_glmfit to do the paired-t analysis. doug On 07/24/2012 01:56 PM, Alexandra Tanner wrote: Hi Doug, Yes, sorry about that! I realized after I'd sent the email to you that I should've sent the email to the freesurfer list as well. We were hoping to look at volume in subcortical regions of the brain -- basal ganglia, hippocampus, amygdala, etc. Do know if there are commands to do the within subjects paired analysis this way? And if so, what they are? Thanks so much! Alex Hi Alexandra, what structure are you looking to analyze? Ie, the volume of what? The volume of cortex? doug ps. In the future, please post such questions to the freesurfer list as it gives others the opportunity to answer and to learn. thanks! On 07/23/2012 12:03 PM, Alexandra Tanner wrote: Hi Mr. Greve, My name is Alex Tanner, I'm the new CRC for Dr. Roffman in the Brain Genomics Lab. I had a question regarding conducting volume analyses. On the freesurfer wiki there are commands that show how to conduct Paired Analyses to look at average surface, and I was curious if it was possible to do a paired analysis looking at volume instead. Any information you have would be very helpful. Thanks so much! Best, Alexandra Tanner Clinical Research Coordinator Laboratory for Brain Genomics Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p) 617.643.3215 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
