Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab
External Email - Use Caution Hi Iglesias, It turns out that my input images are in different orientation and I had a hard time reorienting them. Starting from dicom images and using mri_convert to bring them to nifti format seem to fix the problem The hippocampal subfiled segmentation program with the additional high resolution scan works! Thank you for all the help! Pradeep On Thu, Oct 4, 2018 at 11:28 AM Iglesias Gonzalez, Eugenio < e.igles...@ucl.ac.uk> wrote: > External Email - Use Caution > > Thanks! > > Did you check whether the T2 and the T1 were correctly registered? You can > check out the animated gif under mri/transforms in the subject’s directory. > > Cheers, > > /E > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of Pradeep < > tprad...@gmail.com> > *Reply-To: *Freesurfer support list > *Date: *Thursday, 4 October 2018 at 19:21 > *To: *Freesurfer support list > *Subject: *Re: [Freesurfer] Hippocampal segmentation with an additional > scan ERROR kvlGEMSMatlab > > > > *External Email - Use Caution* > > I have tried this for two subjects and got the same error. > > > > Thanks, > Pradeep > > > > On Thu, Oct 4, 2018 at 11:14 AM Iglesias Gonzalez, Eugenio < > e.igles...@ucl.ac.uk> wrote: > > *External Email - Use Caution* > > Dear Pradeep, > > Did you get this error on several subjects, or only one? > > Cheers, > > /Eugenio > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of Pradeep < > tprad...@gmail.com> > *Reply-To: *Freesurfer support list > *Date: *Thursday, 4 October 2018 at 19:12 > *To: *Freesurfer support list > *Subject: *[Freesurfer] Hippocampal segmentation with an additional scan > ERROR kvlGEMSMatlab > > > > *External Email - Use Caution* > > Hello, > > > > I am trying to run the hippocampal segmentation with an additional Hi-res > scan using the following command > > recon-all -s -hippocampal-subfields-T2 additional scan> > > and got the following error > > > > > > Error using kvlGEMSMatlab > > > /autofs/cluster/koen/eugenio/InsightToolkit-4.9.1/Modules/Core/Common/include/itkImageConstIterator.h:211: > > itk::ERROR: Region ImageRegion (0x7f67011c5dd0) > > Dimension: 3 > > Index: [0, 845, 0] > > Size: [105, 18446744073709550952, 20] > > is outside of buffered region ImageRegion (0x7f6573ca8bb8) > > Dimension: 3 > > Index: [0, 0, 0] > > Size: [526, 181, 526] > > > > Error in kvlReadCroppedImage (line 11) > > Error in segmentSubjectT2_autoEstimateAlveusML (line 838) > > Started at Thu Oct 4 09:35:38 MST 2018 > > Ended at Thu Oct 4 09:57:35 MST 2018 > > #@#%# recon-all-run-time-hours 0.366 > > recon-all -s subject_id finished without error at Thu Oct 4 09:57:36 MST > 2018 > > done > > > > > > I came across a similar error in the forums and using the most recent > version seem to have worked for some, but it did not help in my case. > > > > Freesurfer version I am using > > Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a > > Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a > > > > with matlab run time from 2012b as suggested > > I have also tried to use 2014b runtime which exited right away. > > > > Thank you for your help, > > Pradeep > > > > > > > > > > > > ___ > 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab
External Email - Use Caution I have tried this for two subjects and got the same error. Thanks, Pradeep On Thu, Oct 4, 2018 at 11:14 AM Iglesias Gonzalez, Eugenio < e.igles...@ucl.ac.uk> wrote: > External Email - Use Caution > > Dear Pradeep, > > Did you get this error on several subjects, or only one? > > Cheers, > > /Eugenio > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of Pradeep < > tprad...@gmail.com> > *Reply-To: *Freesurfer support list > *Date: *Thursday, 4 October 2018 at 19:12 > *To: *Freesurfer support list > *Subject: *[Freesurfer] Hippocampal segmentation with an additional scan > ERROR kvlGEMSMatlab > > > > *External Email - Use Caution* > > Hello, > > > > I am trying to run the hippocampal segmentation with an additional Hi-res > scan using the following command > > recon-all -s -hippocampal-subfields-T2 additional scan> > > and got the following error > > > > > > Error using kvlGEMSMatlab > > > /autofs/cluster/koen/eugenio/InsightToolkit-4.9.1/Modules/Core/Common/include/itkImageConstIterator.h:211: > > itk::ERROR: Region ImageRegion (0x7f67011c5dd0) > > Dimension: 3 > > Index: [0, 845, 0] > > Size: [105, 18446744073709550952, 20] > > is outside of buffered region ImageRegion (0x7f6573ca8bb8) > > Dimension: 3 > > Index: [0, 0, 0] > > Size: [526, 181, 526] > > > > Error in kvlReadCroppedImage (line 11) > > Error in segmentSubjectT2_autoEstimateAlveusML (line 838) > > Started at Thu Oct 4 09:35:38 MST 2018 > > Ended at Thu Oct 4 09:57:35 MST 2018 > > #@#%# recon-all-run-time-hours 0.366 > > recon-all -s subject_id finished without error at Thu Oct 4 09:57:36 MST > 2018 > > done > > > > > > I came across a similar error in the forums and using the most recent > version seem to have worked for some, but it did not help in my case. > > > > Freesurfer version I am using > > Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a > > Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a > > > > with matlab run time from 2012b as suggested > > I have also tried to use 2014b runtime which exited right away. > > > > Thank you for your help, > > Pradeep > > > > > > > > > > > ___ > 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
[Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab
External Email - Use Caution Hello, I am trying to run the hippocampal segmentation with an additional Hi-res scan using the following command recon-all -s -hippocampal-subfields-T2 and got the following error Error using kvlGEMSMatlab /autofs/cluster/koen/eugenio/InsightToolkit-4.9.1/Modules/Core/Common/include/itkImageConstIterator.h:211: itk::ERROR: Region ImageRegion (0x7f67011c5dd0) Dimension: 3 Index: [0, 845, 0] Size: [105, 18446744073709550952, 20] is outside of buffered region ImageRegion (0x7f6573ca8bb8) Dimension: 3 Index: [0, 0, 0] Size: [526, 181, 526] Error in kvlReadCroppedImage (line 11) Error in segmentSubjectT2_autoEstimateAlveusML (line 838) Started at Thu Oct 4 09:35:38 MST 2018 Ended at Thu Oct 4 09:57:35 MST 2018 #@#%# recon-all-run-time-hours 0.366 recon-all -s subject_id finished without error at Thu Oct 4 09:57:36 MST 2018 done I came across a similar error in the forums and using the most recent version seem to have worked for some, but it did not help in my case. Freesurfer version I am using Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a with matlab run time from 2012b as suggested I have also tried to use 2014b runtime which exited right away. Thank you for your help, Pradeep ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all | ln -s error
Hello All, My $SUBJECTS_DIR is located on an external disk that was mounted and recon-all exited with errors at ln -s lh.white.preaparc.H lh.white.H I was not able to perform this operation with sudo as well 4172_vsl/surf$ sudo ln -s lh.white.preaparc.H lh.white.H ln: failed to create symbolic link 'lh.white.H': Operation not supported but cp works 4172_vsl/surf$ cp lh.white.preaparc.H lh.white.H has any one come across this problem and what is the best way to fix this? Thanks, Pradeep ___ 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] FS V6.0 gtmseg unsegmented WM
Dear Freesurfers, I am interested us using centrum semiovale as reference region while calculation SUVR values. Is there a way to save the unsegmented white matter [5001& 5002] during the gtmseg step ? in other words looking for an option like this --keep-unsegmented-WM :do not relabel unsegmented_WM as WM Thanks, Pradeep ___ 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] FS V6.0 GTM PVC ROI definition
Its in PET native space. On Wed, Aug 10, 2016 at 2:55 PM Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > which "native" space? the pet native? the anatomical native? > > On 08/09/2016 05:46 PM, Pradeep wrote: > > Hello Doug, > > > > The aux/seg.nii image which has all the ROI's defined does not seem to > > be in the subject's native space or the CVS template space. > > > > How do I bring it to the subjects native space? > > > > Thanks, > > Pradeep > > > > Screenshot from 2016-08-09 14:42:10.png > > > > On Tue, Jul 19, 2016 at 5:03 PM Pradeep <tprad...@gmail.com > > <mailto:tprad...@gmail.com>> wrote: > > > > Thanks responding Doug! > > > > I am interested us using centrum semiovale as reference region. Is > > there a way I can save the unsegmented white matter [5001& 5002] > > during the gtmseg step or what would be its equivalent label in > > the gtm_pvc results table? > > > > Thanks, > > Pradeep > > > > On Thu, Jul 7, 2016 at 11:20 AM Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > wrote: > > > > > > > > On 06/20/2016 08:25 PM, Pradeep wrote: > > > Hello Freesrufer Team, > > > > > > I am trying to use the Partial volume correction procedure > > implemented > > > in the freesurfer 6 beta version and have a few questions. > > > > > > In your recent Neuroimaging paper, the left and right > > hemispheres were > > > combined by taking the average of the two as they did not > > show any > > > age-by-hemisphere interaction. > > > > > > I might have interpreted the Supplementary figure 1 > > incorrectly, but > > > the Geometric transfer matrix seem to show around 52 ROI's, > > So were > > > the L and R ROIs combined for the PVC results you reported > > in that > > > paper? Or were the same 52 used for the general PVC in the > > FS pipeline? > > They were combined only after the PVC calculation. For the > > figure, I > > changed the GTM to show the combined GTM. > > > > > > Do you have any concrete results to examine the effects of > > the size > > > variation over the ROIs used for PVC? > > Not sure what you mean here. You can get the variance > > reduction factor > > for each ROI in the gtm.stats.dat file. This indicates how > > much noise > > reduction you can expect (assuming gaussian noise, etc) in > > each ROI > > given the size and anatomical distribution of the ROIs and PSF. > > > Should a threshold be set for the sizes of these ROIs? > > What do you mean? > > > > > > How were the white matter hypo-intensities dealt with while > > generating > > > the ROI masks? > > I merged them with WM. I tried it with and without, and it did > > not make > > much of a difference. > > doug > > > > > > > > > Thanks, > > > Pradeep > > > > > > > > > > > > ___ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ___ > > Freesur
Re: [Freesurfer] FS V6.0 GTM PVC ROI definition
Thanks responding Doug! I am interested us using centrum semiovale as reference region. Is there a way I can save the unsegmented white matter [5001& 5002] during the gtmseg step or what would be its equivalent label in the gtm_pvc results table? Thanks, Pradeep On Thu, Jul 7, 2016 at 11:20 AM Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > > On 06/20/2016 08:25 PM, Pradeep wrote: > > Hello Freesrufer Team, > > > > I am trying to use the Partial volume correction procedure implemented > > in the freesurfer 6 beta version and have a few questions. > > > > In your recent Neuroimaging paper, the left and right hemispheres were > > combined by taking the average of the two as they did not show any > > age-by-hemisphere interaction. > > > > I might have interpreted the Supplementary figure 1 incorrectly, but > > the Geometric transfer matrix seem to show around 52 ROI's, So were > > the L and R ROIs combined for the PVC results you reported in that > > paper? Or were the same 52 used for the general PVC in the FS pipeline? > They were combined only after the PVC calculation. For the figure, I > changed the GTM to show the combined GTM. > > > > Do you have any concrete results to examine the effects of the size > > variation over the ROIs used for PVC? > Not sure what you mean here. You can get the variance reduction factor > for each ROI in the gtm.stats.dat file. This indicates how much noise > reduction you can expect (assuming gaussian noise, etc) in each ROI > given the size and anatomical distribution of the ROIs and PSF. > > Should a threshold be set for the sizes of these ROIs? > What do you mean? > > > > How were the white matter hypo-intensities dealt with while generating > > the ROI masks? > I merged them with WM. I tried it with and without, and it did not make > much of a difference. > doug > > > > > > Thanks, > > Pradeep > > > > > > > > ___ > > 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 > > > 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 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] Applying the lta transformation to PET image | mri_coreg | mri_segstats
Hello All, I am trying to extract the SUV values a PET image mri_segstats --seg wmparc.mgz --sum petsuv.segstats.dat --i rPET --ctab-default since rPET is supposed to be coregistered to MRI, I did the following mri_coreg --s MRI --mov PET --lta mri_coreg.lta which did not generate the coregistered image but just transformation. Is there a way to generate this image or to just input the mri_coreg.lta as a flag to mri_segstats? Thanks, Pradeep ___ 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] FS V6.0 GTM PVC ROI definition
Thank you! I will. On Mon, Jun 20, 2016, 7:00 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Pradeep > > Doug is on vacation and is the best one to answer your question. If you > don't get a response in a week or 10 days can you repost? > > thanks > Bruce > On Tue, 21 Jun > 2016, Pradeep wrote: > > > Hello Freesrufer Team, > > > > I am trying to use the Partial volume correction procedure implemented in > > the freesurfer 6 beta version and have a few questions. > > > > In your recent Neuroimaging paper, the left and right hemispheres were > > combined by taking the average of the two as they did not show any > > age-by-hemisphere interaction. > > > > I might have interpreted the Supplementary figure 1 incorrectly, but the > > Geometric transfer matrix seem to show around 52 ROI's, So were the L > and R > > ROIs combined for the PVC results you reported in that paper? Or were > the > > same 52 used for the general PVC in the FS pipeline? > > > > Do you have any concrete results to examine the effects of the size > > variation over the ROIs used for PVC? Should a threshold be set for the > > sizes of these ROIs? > > > > How were the white matter hypo-intensities dealt with while generating > the > > ROI masks? > > > > > > Thanks, > > Pradeep > > > > > >___ > 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 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] FS V6.0 GTM PVC ROI definition
Hello Freesrufer Team, I am trying to use the Partial volume correction procedure implemented in the freesurfer 6 beta version and have a few questions. In your recent Neuroimaging paper, the left and right hemispheres were combined by taking the average of the two as they did not show any age-by-hemisphere interaction. I might have interpreted the Supplementary figure 1 incorrectly, but the Geometric transfer matrix seem to show around 52 ROI's, So were the L and R ROIs combined for the PVC results you reported in that paper? Or were the same 52 used for the general PVC in the FS pipeline? Do you have any concrete results to examine the effects of the size variation over the ROIs used for PVC? Should a threshold be set for the sizes of these ROIs? How were the white matter hypo-intensities dealt with while generating the ROI masks? Thanks, Pradeep ___ 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] Reading values from overlays with PETcoreg
Hello Doug, I was wondering if there is a flag in the command to obtain the SUVRs for the same ROIs with out partial volume correction so that it would be easier to compare. Thanks, Pradeep On Fri, Jan 29, 2016 at 1:30 PM, Pradeep <tprad...@gmail.com> wrote: > It worked! Thank you! > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > gtmseg.mgz --reg output.lta --replace-file seg.replace251.list --rescale > 251 --mgx 0.01 --o gtmpvcRcc.output > > On Fri, Jan 29, 2016 at 12:23 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> The problem is that --default-seg-merge merges the CC with WM, so you >> can't use that option, which means that you'll have to specify the rest >> of the default seg merge manually. You can do this with more --replace >> args or you can create a file. If you've been able to run mri_gtmpvc >> without the current replace, then it will create a replacement file in >> the aux folder. Get that, remove the 251 entry, and change the 252-255 >> entries to point to 251 >> >> On 01/29/2016 02:12 PM, Pradeep wrote: >> > Unfortunately, that did not fix the problem. >> > >> > Here is what I did >> > 1)gtmseg --s 128_S_0225_v06 --keep-cc # noerrors >> > 2)gtmseg --s 128_S_0225_v06 --keep-cc --no-xcerseg # no errors >> > >> > 3)mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg >> > gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 >> > --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o >> > gtmpvcrcc.output >> > Loading input t12pet.nii.gz >> > done loading input 1 frames >> > ERROR: item 251 appears as both source and target seg id in >> > replacement list >> > >> > $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ >> > setenv SUBJECTS_DIR /analysis/software_test/fs6pvc >> > cd /analysis/software_test/fs6pvc/128_S_0225_v06/mri >> > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg >> > gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 >> > --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o >> > gtmpvcrcc.output >> > sysname Linux >> > hostname >> > machine x86_64 >> > user >> > vgthresh 0.001000 >> > nReplace 22 >> > 0. 0. 0. 0. 0. 0. >> > 9 avail.processors, using 9 >> > Creating output directory gtmpvcrcc.output >> > Loading seg for gtm gtmseg.mgz >> > Loading seg ctab gtmseg.ctab >> > Reading gtmseg.lta >> > Replacing 22 >> > ERROR: CheckSegTissueType() no entry for seg 192 >> > Failed tissue type check >> > >> > Thank you for looking into this, >> > Pradeep >> > >> > >> > On Fri, Jan 29, 2016 at 10:13 AM, Douglas N Greve >> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> > >> > I think I see the problem. When you run gtmseg, you need to add >> > --keep-cc. You can rerun it using the previous command line, but add >> > --keep-cc and --no-xcerseg. The second option tells it not to redo >> the >> > extracerebral segmentation (which won't change with CC) >> > >> > On 01/29/2016 11:21 AM, Pradeep wrote: >> > > Thank you for the response. >> > > >> > > Here is my full command log with error >> > > >> > > >> > > $gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc >> > > >> > > $ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 >> --seg >> > > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o >> > > gtmpvccc.output >> > > Loading input t12pet.nii.gz >> > > done loading input 1 frames >> > > >> > > $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ >> > > setenv SUBJECTS_DIR /analysis/software_test/fs6pvc >> > > cd /analysis/software_test/fs6pvc/**/mri >> > > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg >> > > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o >> > > gtmpvccc.output >> > > sysname Linux >> > > hostname server >> > > machine x86_64 >> > > user user >> > > vgthresh 0.001000 >> > > nReplace 18 >>
Re: [Freesurfer] bbregister problems
Thank you Douglas!
mri_coreg did an awesome job and the registration look good.
On Mon, Feb 22, 2016 at 7:51 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> If you have spm, you can use --init-spm. Alternatively, you can use
> mri_coreg instead of bbr (bbr is not as effective on blurry data)
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
>
> mri_coreg --s $fs --mov ${pet_ext}_LIA.nii --lta output.lta
>
> Also, why is the top of the head cut off? That makes it much more
> difficult to register.
>
> doug
>
>
>
>
> On 2/22/16 8:02 PM, Pradeep wrote:
>
> Hello All,
>
> I am trying to map pet scans to MRI using bbregister and quite a few
> subjects were improperly registered.
>
> Here are my steps:
> bbregister --s $fs --mov ${pet_ext}_LIA.nii --init-fsl --t1 --lta
> output.lta
> tkregister2 --mov summed_LIA.nii --reg output.dat --surf
>
>
> [ mri]$ more output.dat.mincost
> 0.860663 0.000513 0.000492 -11.863233
> The first value is quite close to 1 so its bad
>
> I have attached a screen shot of the image and the log file generated
> after bbregister.
> Please let me know if there are any parameters that I could tweak to make
> the registration better.
>
> Thank you for your help,
> -Pradeep
>
>
>
> ___
> Freesurfer mailing
> listfreesur...@nmr.mgh.harvard.eduhttps://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 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] Reading values from overlays with PETcoreg
Thank you for the response. Here is my full command log with error $gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc $ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o gtmpvccc.output Loading input t12pet.nii.gz done loading input 1 frames $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ setenv SUBJECTS_DIR /analysis/software_test/fs6pvc cd /analysis/software_test/fs6pvc/**/mri mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o gtmpvccc.output sysname Linux hostname server machine x86_64 user user vgthresh 0.001000 nReplace 18 0. 0. 0. 0. 0. 0. 9 avail.processors, using 9 Creating output directory gtmpvccc.output Loading seg for gtm gtmseg.mgz Loading seg ctab gtmseg.ctab Reading gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() no entry for seg 192 Failed tissue type check Thanks, Pradeep On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > > On 01/28/2016 06:50 PM, Pradeep wrote: > > Hello Doug, > > > > I have used the gtmseg with --keep-cc flag and the corresponding ctab > > files showed the labels but the mri_gtmpvc step failed. > > > > Loading seg for gtm gtmseg.mgz > > Loading seg ctab gtmseg.ctab > > Reading gtmseg.lta > > Replacing 18 > > ERROR: CheckSegTissueType() no entry for seg 192 > > Failed tissue type check > > > What is your mri_gtmpvc command line? What is the rest of the terminal > output? > > My objective is to use the combination of all CC's as a reference > > region and obtain the PVC results, which would be listed in gtm.stats.dat > It will be best to combine them when running mri_gtmpvc using --replace, > eg, --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 > this will cause all segments of the CC to appear to be a single segment > (251). > > > > Also, I read in the previous email discussions that the default > > ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR with > > another ROI as a reference region, > > would it be OK take a ratio of the ROI's in gtm.stats.dat table. > Yes, or you can spec the new region, eg --rescale 251 > > > > Thanks, > > Pradeep > > > > On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > > > If you want to use partial volume correction, then you are better off > > using mri_gtmpvc with the bbr registration, something like > > > > 1. To start, run > > > > gtmseg --s subject > > > > This will take a couple of hours and produces some files needed > > for GTM > > PVC (which is used for GTM, MG, RBV). > > > > 2. You'd then register the PET to the anatomical with bbregister > > (probably with --t2 weighting). Make sure to save the output as an > LTA > > (--lta). I usually use the mean TAC as the input. You can do this in > > parallel with #1. > > > > 3. You'd then run mri_gtmpvc, something like > > > > mri_gtmpvc --i pet.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg > > gtmseg.mgz > > --reg reg.lta --default-seg-merge --o gtmpvc.output > > > > PSF is the point-spread FWHM of the scanner; reg.lta is the > > registration from #2. By default, this will scale by pons. The output > > will be gtm.stats.dat and gtm.nii.gz. They both basically have the > > same information. gtm.stats.dat is an easy to read text file. Where > > each row is an ROI, something like: > > > > 9 17 Left-Hippocampussubcort_gm 473 > > 174.0831.406 0.1216 > > > > 9 = nineth row > > 17 = index for RO > > Left-Hippocampus = name of ROI > > subcort_gm = tissue class > > 473 = number of PET voxels in the ROI > > 174 = variance reduction factor for ROI (based on GLM/SGTM) > > 1.406 = PVC uptake of ROI relative to Pons > > 0.1216 = resdiual varaince across voxels in the ROI > > > > gtm.nii.gz is a nifti file with each "voxel" being an ROI. The value > > is the PVC uptake of ROI relative to Pons. These can easily be > > concatenated together (mri_concat) and used as input to mri_glmfit > > for group analysis. > > > > > > > > > > On 01/08/2016 04:22 AM, Benjamin Spurny wrote: > > > Dear Freesurfer experts! > &
Re: [Freesurfer] Reading values from overlays with PETcoreg
Unfortunately, that did not fix the problem. Here is what I did 1)gtmseg --s 128_S_0225_v06 --keep-cc # noerrors 2)gtmseg --s 128_S_0225_v06 --keep-cc --no-xcerseg # no errors 3)mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o gtmpvcrcc.output Loading input t12pet.nii.gz done loading input 1 frames ERROR: item 251 appears as both source and target seg id in replacement list $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ setenv SUBJECTS_DIR /analysis/software_test/fs6pvc cd /analysis/software_test/fs6pvc/128_S_0225_v06/mri mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o gtmpvcrcc.output sysname Linux hostname machine x86_64 user vgthresh 0.001000 nReplace 22 0. 0. 0. 0. 0. 0. 9 avail.processors, using 9 Creating output directory gtmpvcrcc.output Loading seg for gtm gtmseg.mgz Loading seg ctab gtmseg.ctab Reading gtmseg.lta Replacing 22 ERROR: CheckSegTissueType() no entry for seg 192 Failed tissue type check Thank you for looking into this, Pradeep On Fri, Jan 29, 2016 at 10:13 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > I think I see the problem. When you run gtmseg, you need to add > --keep-cc. You can rerun it using the previous command line, but add > --keep-cc and --no-xcerseg. The second option tells it not to redo the > extracerebral segmentation (which won't change with CC) > > On 01/29/2016 11:21 AM, Pradeep wrote: > > Thank you for the response. > > > > Here is my full command log with error > > > > > > $gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc > > > > $ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o > > gtmpvccc.output > > Loading input t12pet.nii.gz > > done loading input 1 frames > > > > $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ > > setenv SUBJECTS_DIR /analysis/software_test/fs6pvc > > cd /analysis/software_test/fs6pvc/**/mri > > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o > > gtmpvccc.output > > sysname Linux > > hostname server > > machine x86_64 > > user user > > vgthresh 0.001000 > > nReplace 18 > > 0. 0. 0. 0. 0. 0. > > 9 avail.processors, using 9 > > Creating output directory gtmpvccc.output > > Loading seg for gtm gtmseg.mgz > > Loading seg ctab gtmseg.ctab > > Reading gtmseg.lta > > Replacing 18 > > ERROR: CheckSegTissueType() no entry for seg 192 > > Failed tissue type check > > > > > > Thanks, > > Pradeep > > > > > > On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > > > > > On 01/28/2016 06:50 PM, Pradeep wrote: > > > Hello Doug, > > > > > > I have used the gtmseg with --keep-cc flag and the > > corresponding ctab > > > files showed the labels but the mri_gtmpvc step failed. > > > > > > Loading seg for gtm gtmseg.mgz > > > Loading seg ctab gtmseg.ctab > > > Reading gtmseg.lta > > > Replacing 18 > > > ERROR: CheckSegTissueType() no entry for seg 192 > > > Failed tissue type check > > > > > What is your mri_gtmpvc command line? What is the rest of the > terminal > > output? > > > My objective is to use the combination of all CC's as a reference > > > region and obtain the PVC results, which would be listed in > > gtm.stats.dat > > It will be best to combine them when running mri_gtmpvc using > > --replace, > > eg, --replace 252 251 --replace 253 251 --replace 254 251 > > --replace 255 251 > > this will cause all segments of the CC to appear to be a single > > segment > > (251). > > > > > > Also, I read in the previous email discussions that the default > > > ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR > with > > > another ROI as a reference region, > > > would it be OK take a ratio of the ROI's in gtm.stats.dat table. > > Yes, or you can spec the new region, eg --
Re: [Freesurfer] Reading values from overlays with PETcoreg
It worked! Thank you! mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --replace-file seg.replace251.list --rescale 251 --mgx 0.01 --o gtmpvcRcc.output On Fri, Jan 29, 2016 at 12:23 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > The problem is that --default-seg-merge merges the CC with WM, so you > can't use that option, which means that you'll have to specify the rest > of the default seg merge manually. You can do this with more --replace > args or you can create a file. If you've been able to run mri_gtmpvc > without the current replace, then it will create a replacement file in > the aux folder. Get that, remove the 251 entry, and change the 252-255 > entries to point to 251 > > On 01/29/2016 02:12 PM, Pradeep wrote: > > Unfortunately, that did not fix the problem. > > > > Here is what I did > > 1)gtmseg --s 128_S_0225_v06 --keep-cc # noerrors > > 2)gtmseg --s 128_S_0225_v06 --keep-cc --no-xcerseg # no errors > > > > 3)mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > > gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 > > --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o > > gtmpvcrcc.output > > Loading input t12pet.nii.gz > > done loading input 1 frames > > ERROR: item 251 appears as both source and target seg id in > > replacement list > > > > $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ > > setenv SUBJECTS_DIR /analysis/software_test/fs6pvc > > cd /analysis/software_test/fs6pvc/128_S_0225_v06/mri > > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > > gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 > > --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o > > gtmpvcrcc.output > > sysname Linux > > hostname > > machine x86_64 > > user > > vgthresh 0.001000 > > nReplace 22 > > 0. 0. 0. 0. 0. 0. > > 9 avail.processors, using 9 > > Creating output directory gtmpvcrcc.output > > Loading seg for gtm gtmseg.mgz > > Loading seg ctab gtmseg.ctab > > Reading gtmseg.lta > > Replacing 22 > > ERROR: CheckSegTissueType() no entry for seg 192 > > Failed tissue type check > > > > Thank you for looking into this, > > Pradeep > > > > > > On Fri, Jan 29, 2016 at 10:13 AM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > I think I see the problem. When you run gtmseg, you need to add > > --keep-cc. You can rerun it using the previous command line, but add > > --keep-cc and --no-xcerseg. The second option tells it not to redo > the > > extracerebral segmentation (which won't change with CC) > > > > On 01/29/2016 11:21 AM, Pradeep wrote: > > > Thank you for the response. > > > > > > Here is my full command log with error > > > > > > > > > $gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc > > > > > > $ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > > > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o > > > gtmpvccc.output > > > Loading input t12pet.nii.gz > > > done loading input 1 frames > > > > > > $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ > > > setenv SUBJECTS_DIR /analysis/software_test/fs6pvc > > > cd /analysis/software_test/fs6pvc/**/mri > > > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > > > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o > > > gtmpvccc.output > > > sysname Linux > > > hostname server > > > machine x86_64 > > > user user > > > vgthresh 0.001000 > > > nReplace 18 > > > 0. 0. 0. 0. 0. 0. > > > 9 avail.processors, using 9 > > > Creating output directory gtmpvccc.output > > > Loading seg for gtm gtmseg.mgz > > > Loading seg ctab gtmseg.ctab > > > Reading gtmseg.lta > > > Replacing 18 > > > ERROR: CheckSegTissueType() no entry for seg 192 > > > Failed tissue type check > > > > > > > > > Thanks, > > > Pradeep > > > > > > > > > On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve > > > <g
Re: [Freesurfer] Reading values from overlays with PETcoreg
Hello Doug, I have used the gtmseg with --keep-cc flag and the corresponding ctab files showed the labels but the mri_gtmpvc step failed. Loading seg for gtm gtmseg.mgz Loading seg ctab gtmseg.ctab Reading gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() no entry for seg 192 Failed tissue type check My objective is to use the combination of all CC's as a reference region and obtain the PVC results, which would be listed in gtm.stats.dat Also, I read in the previous email discussions that the default ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR with another ROI as a reference region, would it be OK take a ratio of the ROI's in gtm.stats.dat table. Thanks, Pradeep On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > If you want to use partial volume correction, then you are better off > using mri_gtmpvc with the bbr registration, something like > > 1. To start, run > > gtmseg --s subject > > This will take a couple of hours and produces some files needed for GTM > PVC (which is used for GTM, MG, RBV). > > 2. You'd then register the PET to the anatomical with bbregister > (probably with --t2 weighting). Make sure to save the output as an LTA > (--lta). I usually use the mean TAC as the input. You can do this in > parallel with #1. > > 3. You'd then run mri_gtmpvc, something like > > mri_gtmpvc --i pet.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg gtmseg.mgz > --reg reg.lta --default-seg-merge --o gtmpvc.output > > PSF is the point-spread FWHM of the scanner; reg.lta is the > registration from #2. By default, this will scale by pons. The output > will be gtm.stats.dat and gtm.nii.gz. They both basically have the > same information. gtm.stats.dat is an easy to read text file. Where > each row is an ROI, something like: > > 9 17 Left-Hippocampussubcort_gm 473 > 174.0831.406 0.1216 > > 9 = nineth row > 17 = index for RO > Left-Hippocampus = name of ROI > subcort_gm = tissue class > 473 = number of PET voxels in the ROI > 174 = variance reduction factor for ROI (based on GLM/SGTM) > 1.406 = PVC uptake of ROI relative to Pons > 0.1216 = resdiual varaince across voxels in the ROI > > gtm.nii.gz is a nifti file with each "voxel" being an ROI. The value > is the PVC uptake of ROI relative to Pons. These can easily be > concatenated together (mri_concat) and used as input to mri_glmfit > for group analysis. > > > > > On 01/08/2016 04:22 AM, Benjamin Spurny wrote: > > Dear Freesurfer experts! > > > > I am currently working on PET analysis using FS > > > > I coregistered my PET with the processed MR using bbregister, > > transfered it to a surface using mri_vol2surf > > and now createt an overlay in freeview with the lh.inflated and used the > > labels from the lh.aparc.a2009s.annot file. > > > > In freeview i get the corresponding BP value for each vertex now but > > is there a way to get a list of vertices with the corresponding BP value > > and the corresponding ROI this vertex belongs to? > > Or is there a better to do this analyis? > > > > Many thanks in advance! > > > > Benjamin > > > > ___ > > 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 > > > 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 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] PET tools in FS dev v6.0
Thank you for the response Doug! The PET images I have are static images. Six * 5 min frames which I have summed together after realigning. mri_gtmpvc --i summed.nii --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o gtmpvc.output This command has worked and I just wanted to conform if it the correct way to use it. -Pradeep On Wed, Nov 18, 2015 at 10:41 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > For single frame, you can just run > mri_convert input.nii output.nii --frame F > where F is the 0-based frame number, then run mri_gtmpvc on output.nii > > The PVC "image" is a bit tricky. You can get a muller-gartner image > (--mgx) or region-based voxel-wise (RBV) image with --rbv. > > > > On 11/18/2015 12:36 PM, Pradeep wrote: > > Hello Doug, > > > > I am in the process of testing the FS PVC procedure and I was > > wondering if there is a way to do this procedure with single frame PET > > data and get the partial volume corrected SUVR image. I know that this > > is still new and not all the processes is documented yet, but any > > inputs on this would be appreciated. I have successfully ran steps 1 > > and 2 from the process you have outlines above. > > > > Thanks, > > Pradeep > > > > On Mon, Sep 28, 2015 at 10:03 PM, Jonathan DuBois > > <jonathan.m.dub...@gmail.com <mailto:jonathan.m.dub...@gmail.com>> > wrote: > > > > Hi Doug, > > > > I uploaded the files you requested. I'm not sure if it matters, > > but one thing I forgot to mention was that in order to get the pet > > file in the right format and orientation, I ended up using > > (ecattominc pet.v pet.mnc) and (itk_convert --inv-y --inv-x > > pet.mnc pet.nii). I couldn't find a good tool to convert directly > > form ECAT to NIFTI, but perhaps this conversion process interferes > > with the pet processing? > > > > Best, > > Jonathan > > > > Message: 7 > > Date: Mon, 28 Sep 2015 18:07:18 -0400 > > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>> > > Subject: Re: [Freesurfer] PET tools in FS dev v6.0 > > To: freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu>Message-ID: > > <5609ba16.2090...@nmr.mgh.harvard.edu > > <mailto:5609ba16.2090...@nmr.mgh.harvard.edu>> > > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > Can you upload the FS subject, pet data, and .lta? > > https://gate.nmr.mgh.harvard.edu/filedrop2 > > > > > > > > On 09/28/2015 12:08 PM, Jonathan DuBois wrote: > > > Hi Doug, > > > > > > I was told you were away last week so I'm reposting this > message. > > > Thanks for sending me the information on the PET scripts. I > > > ran gtmseg, and bbregister successfully (I inspected both and > they > > > look accurate), but I am getting a segfault with mri_gtmpvc at > the > > > auto mask step. > > > > > > I copied the command and the error below. I thought that it > could be a > > > memory issue due to the size of the matrix (I ran it on a mac > with > > > 8gb) but I also tried to run it with the --tt-reduce and got > the same > > > error. The data is from an HRRT PET scanner with a PSF of 4mm. > For the > > > auto-mask input I used 6 .01, as your instructions were PSF+2. > Is this > > > correct? > > > > > > Thanks > > > Jonathan > > > > > > mri_gtmpvc --i pet.nii.gz --psf 4 --auto-mask 6 .01 --seg > > > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz > --reg > > > pet_avt_reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output > > > --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale > > > Loading input pet.nii.gz > > > done loading input 26 frames > > > > > > $Id: mri_gtmpvc.c,v 1.57 2015/05/29 19:51:24 greve Exp $ > > > setenv SUBJECTS_DIR /Users/jonathandubois/data/fssub > > > cd /Volumes/my_passport/external/Documents/fssub2/test > > > mri_gtmpvc --i pet.nii.gz --psf 4 --auto-mask 6 .01 --seg > > > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz
Re: [Freesurfer] PET tools in FS dev v6.0
Hello Doug, I am in the process of testing the FS PVC procedure and I was wondering if there is a way to do this procedure with single frame PET data and get the partial volume corrected SUVR image. I know that this is still new and not all the processes is documented yet, but any inputs on this would be appreciated. I have successfully ran steps 1 and 2 from the process you have outlines above. Thanks, Pradeep On Mon, Sep 28, 2015 at 10:03 PM, Jonathan DuBois < jonathan.m.dub...@gmail.com> wrote: > Hi Doug, > > I uploaded the files you requested. I'm not sure if it matters, but one > thing I forgot to mention was that in order to get the pet file in the > right format and orientation, I ended up using (ecattominc pet.v pet.mnc) > and (itk_convert --inv-y --inv-x pet.mnc pet.nii). I couldn't find a good > tool to convert directly form ECAT to NIFTI, but perhaps this conversion > process interferes with the pet processing? > > Best, > Jonathan > > >> Message: 7 >> Date: Mon, 28 Sep 2015 18:07:18 -0400 >> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] PET tools in FS dev v6.0 >> To: freesurfer@nmr.mgh.harvard.edu >> Message-ID: <5609ba16.2090...@nmr.mgh.harvard.edu> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >> Can you upload the FS subject, pet data, and .lta? >> https://gate.nmr.mgh.harvard.edu/filedrop2 >> >> >> >> On 09/28/2015 12:08 PM, Jonathan DuBois wrote: >> > Hi Doug, >> > >> > I was told you were away last week so I'm reposting this message. >> > Thanks for sending me the information on the PET scripts. I >> > ran gtmseg, and bbregister successfully (I inspected both and they >> > look accurate), but I am getting a segfault with mri_gtmpvc at the >> > auto mask step. >> > >> > I copied the command and the error below. I thought that it could be a >> > memory issue due to the size of the matrix (I ran it on a mac with >> > 8gb) but I also tried to run it with the --tt-reduce and got the same >> > error. The data is from an HRRT PET scanner with a PSF of 4mm. For the >> > auto-mask input I used 6 .01, as your instructions were PSF+2. Is this >> > correct? >> > >> > Thanks >> > Jonathan >> > >> > mri_gtmpvc --i pet.nii.gz --psf 4 --auto-mask 6 .01 --seg >> > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz --reg >> > pet_avt_reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output >> > --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale >> > Loading input pet.nii.gz >> > done loading input 26 frames >> > >> > $Id: mri_gtmpvc.c,v 1.57 2015/05/29 19:51:24 greve Exp $ >> > setenv SUBJECTS_DIR /Users/jonathandubois/data/fssub >> > cd /Volumes/my_passport/external/Documents/fssub2/test >> > mri_gtmpvc --i pet.nii.gz --psf 4 --auto-mask 6 .01 --seg >> > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz --reg >> > pet_avt_reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output >> > --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale >> > sysname Darwin >> > hostname Jons-MacBook-Air.local >> > machine x86_64 >> > user jonathandubois >> > vgthresh 0.001000 >> > nReplace 18 >> > 0. 0. 0. 0. 0. 0. >> > 4 avail.processors, using 1 >> > Creating output directory gtmpvc.output >> > Loading seg for gtm >> > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz >> > Loading seg ctab >> > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.ctab >> > Reading /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.lta >> > Replacing 18 >> > Pruning ctab >> > done with seg vol >> > maxFWHM = 3.28205 (voxels), PadThresh=0.0001, nPad=10 >> > Computing auto mask >> > Segmentation fault: 11 >> > >> > >> > Message: 13 >> > Date: Tue, 08 Sep 2015 14:34:11 -0400 >> > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu >> > <mailto:gr...@nmr.mgh.harvard.edu>> >> > Subject: Re: [Freesurfer] PET tools in FS dev v6.0 >> > To: freesurfer@nmr.mgh.harvard.edu >> > <mailto:freesurfer@nmr.mgh.harvard.edu>Message-ID: >> > <55ef2a23.3070...@nmr.mgh.harvard.edu >> > <mailto:55ef2a23.3070...@nmr.mgh.harvard.edu>> >> > Content-Type: text/plain; charset=windows-1252; format=flowed >> > Yes there are both. For KM we have MRTM1 and MRTM
[Freesurfer] Longitudinal Freesurfer | BA labels does not change
Hello All, I ran the freesurfer longitudinal stream for a subject with three time points and found that the /stats/lh.BA.stats has remained constant across all time points where as aseg.stats showed variations. Sorry if this question is too nieve. Thanks, Pradeep ___ 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] Advice - best method, longitudinal vs. cross-sectional
Thanks you for the reply. Martin, the scans are 0,14 and 21 days a part. I will run a few more subjects and check the results as you suggested. On Fri, Apr 17, 2015 at 8:59 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: you should also plot them on the same axes (or at the very least with the same limits) On Fri, 17 Apr 2015, Martin Reuter wrote: Hi Pradeep, is this the result of a single subject? In a single subject lot's of things can happen (e.g. motion artefacts can affect a single time point, other imaging or measurement noise will have effects). Also how far are the time points apart? Run the same thing with 20 subjects and you should see significantly reduced variablility in the longitudinal stream vs the cross sectional one. Best, Martin On 04/16/2015 01:12 PM, Pradeep wrote: Hello All, I have pre-processed a subject that has T1 scans at 3 time points using the freesurfer cross-sectional and longitudinal methods. The results show a lot of variability. I have attached the plots. Any advice would be much appreciated. Thanks, Pradeep On Wed, Apr 15, 2015 at 5:26 PM, Pradeep tprad...@gmail.com wrote: Hello All, I have pre-processed a subject that has T1 scans at 3 time using the freesurfer cross-sectional and longitudinal methods. The results show a lot of variability. I have attached the plots. Any advice would be much appreciated. Thanks, Pradeep On Wed, Jun 4, 2014 at 12:03 PM, Alexandru Hanganu al.hang...@yahoo.ca wrote: Thank you very much for your answer Bruce ! have a nice evening, Alex. Le 3 juin 14 7:6, Bruce Fischl a écrit : Hi Alex I would think that longitudinal analysis is still the way to go as we try to improve both reliability and sensitivity using the fact that we have multiple scans/subject. cheers Bruce On Tue, 3 Jun 2014, Alexandru Hanganu wrote: Hello Everyone, could someone please give us an advice about which method you consider is the best for our study ? we have two groups with MRI at Time 1. Each group received medication. After this we performed another MRI at Time 2 after 2 weeks. The best method for this study is a longitudinal one or a cross-sectional GLM ? We consider that the distance between the time points is too small, and the longitudinal method is not the best choice. Hence, this study should be treated as a cross-sectional one. In this case we think about performing a simple GLM with the contrasts: 0.5 0.5 0.5 0.5 or 1 -1 -1 1 for the groups: 1) grp 1 time 1 2) grp 1 time 2 3) grp 2 time 1 4) grp 2 time 2 we are searching to see whether medication had any impact on the cortical morphology in each group and between the groups. Thank you ! Best regards, 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 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 ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman
Re: [Freesurfer] Advice - best method, longitudinal vs. cross-sectional
Hello All, I have pre-processed a subject that has T1 scans at 3 time points using the freesurfer cross-sectional and longitudinal methods. The results show a lot of variability. I have attached the plots. Any advice would be much appreciated. Thanks, Pradeep On Wed, Apr 15, 2015 at 5:26 PM, Pradeep tprad...@gmail.com wrote: Hello All, I have pre-processed a subject that has T1 scans at 3 time using the freesurfer cross-sectional and longitudinal methods. The results show a lot of variability. I have attached the plots. Any advice would be much appreciated. Thanks, Pradeep On Wed, Jun 4, 2014 at 12:03 PM, Alexandru Hanganu al.hang...@yahoo.ca wrote: Thank you very much for your answer Bruce ! have a nice evening, Alex. Le 3 juin 14 7:6, Bruce Fischl a écrit : Hi Alex I would think that longitudinal analysis is still the way to go as we try to improve both reliability and sensitivity using the fact that we have multiple scans/subject. cheers Bruce On Tue, 3 Jun 2014, Alexandru Hanganu wrote: Hello Everyone, could someone please give us an advice about which method you consider is the best for our study ? we have two groups with MRI at Time 1. Each group received medication. After this we performed another MRI at Time 2 after 2 weeks. The best method for this study is a longitudinal one or a cross-sectional GLM ? We consider that the distance between the time points is too small, and the longitudinal method is not the best choice. Hence, this study should be treated as a cross-sectional one. In this case we think about performing a simple GLM with the contrasts: 0.5 0.5 0.5 0.5 or 1 -1 -1 1 for the groups: 1) grp 1 time 1 2) grp 1 time 2 3) grp 2 time 1 4) grp 2 time 2 we are searching to see whether medication had any impact on the cortical morphology in each group and between the groups. Thank you ! Best regards, 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 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.
Re: [Freesurfer] Creation of the aseg.stats table fails when only running -autorecon1 or -autorecon2
Hi Roberto, I had the same problem, you need to re run the recon process using recon-all -s subjid -cortribbon. Hope it helps Pradeep. On Fri, Feb 6, 2015 at 6:37 PM, Roberto Medeiros de Souza roberto.medeiros.so...@gmail.com wrote: Hi, I'm knew to FreeSurfer. I am using the stable v5.3 and I am having the known issue about Creation of the aseg.stats table fails when only running -autorecon1 or -autorecon2 because ribbon.mgz is not present. The FreeSurfer page ( https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) says that this problem has been solved and that I should ask for a patch. Does anyone knows where I can get this patch? Thanks in advance! Roberto Medeiros de Souza ___ 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. -- Pradeep Kumar Mahato ___ 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] Converting dicom images to nifti
Hi experts, I am trying to convert dicom images namely 00A0,00A1,00A2 [ No file extension ] etc. These are generated by Philips machine. I used dcm2nii, it does not give correct result. It gives warning : this software will only convert the first slice of this multislice lossless compressed JPEG . In one thread I read that dicom images from Philips scanner are oriented differently. I tried to use dcmunpack method, but I am not able to save the converted image. I used dcmunpack -src srcDirc. Please share the correct procedure. In one of the subjects I have very less number of images:30. Is it necessary to have more dicom images to have a better brain mri image . If yes, what should be the optimal number of images Thanking You Pradeep Kumar Mahato ___ 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] Converting dicom images to nifti
Please tell how to use dcmunpack. Any help converting dicom to nii. On Jan 27, 2015 9:03 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Hi Pradeep, I don't think that we can convert that either. Sorry. doug On 1/27/15 7:18 AM, pradeep mahato wrote: Hi experts, I am trying to convert dicom images namely 00A0,00A1,00A2 [ No file extension ] etc. These are generated by Philips machine. I used dcm2nii, it does not give correct result. It gives warning : this software will only convert the first slice of this multislice lossless compressed JPEG . In one thread I read that dicom images from Philips scanner are oriented differently. I tried to use dcmunpack method, but I am not able to save the converted image. I used dcmunpack -src srcDirc. Please share the correct procedure. In one of the subjects I have very less number of images:30. Is it necessary to have more dicom images to have a better brain mri image . If yes, what should be the optimal number of images Thanking You Pradeep Kumar Mahato ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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 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] Creating a .gca file
Hello experts, I am using rebuild_gca_atlas.csh,v 1.22 2011/03/02 20:16:39. I am trying to create a atlas using previous registered subjects. It does not complete the mri_ca_normalize phase and stops there. It shows pbsubmit: Command not found as error. Please correct me. Also attaching the rebuild_gca_atlas file. Thanks Pradeep Kumar Mahato rebuild_gca_atlas.csh Description: C-Shell script ___ 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] 3D image for any region of interest
Hello experts, How to view 3D image of hippocampus or any region of interest. Thanking you Pradeep Kumar Mahato ___ 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] Running separate recon-all for each hemisphere
Hello experts, I ran recon-all -all -hemi lh -ssubjectid, it failed due to some rh.white file missing . Can someone tell me how i can run autorecon1 , autorecon2 and autorecon3 separately for each hemisphere. And also can I run the reconstruction process for left and right hemisphere parallely. How much time can we save running each hemisphere parallely. Thanking you Pradeep Kumar Mahato ___ 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] Performance of Broadwell and Haswell processors
Hi Nick, Can you tell me what would be best processing time to do recon-all process on one brain mri image using a high end machine ( Servers ) or using GPU based machine. We have more than 1000 of brain mri images, processing all these images is the bottleneck now. Pradeep On Tue, Dec 16, 2014 at 6:31 AM, Nick Schmansky, MGH ni...@nmr.mgh.harvard.edu wrote: Pradeep, Our lab will be getting a Haswell-based system soon and will evaluate any speed gains. The system is a Dell PowerEdge R730 with an Intel® Xeon® E5‐2643 v3 3.4GHz processor. N. On Mon, 2014-12-15 at 13:43 +0530, pradeep mahato wrote: Hello everyone, Have anyone used Broadwell or Haswell process for Brain MRI image processing. If used can you please mention the system configuration you are using. How long does it take to run recon-all process for one brain MRI image. Thanking you Pradeep Kumar Mahato ___ 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. -- Pradeep Kumar Mahato ___ 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] Performance of Broadwell and Haswell processors
Hello everyone, Have anyone used Broadwell or Haswell process for Brain MRI image processing. If used can you please mention the system configuration you are using. How long does it take to run recon-all process for one brain MRI image. Thanking you Pradeep Kumar Mahato ___ 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] Difference results due to difference in brain size
Hello Experts, There is a significant differences between a African, Asian or a Caucasian brain size. How does FreeSurfer recon-all performs for these different types of brain. I am doing brain MRI analysis for Asian brain, will the default brain atlas will be ok? If not how do I load another brain atlas in FreeSurfer. Thanking You Pradeep Kumar Mahato ___ 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] Extracting hippocampus
I am running the recon method for oasis recon-all -autorecon1 -autorecon2 -i ./OAS2_0001_MR1/RAW/mpr-1.nifti.img -i ./OAS2_0001_MR1/RAW/mpr-2.nifti.img -i ./OAS2_0001_MR1/RAW/mpr-3.nifti.img -s OAS12_1 The program exited saying ribbon.mgz file is missing. Thus I am unable to get aseg.stats data. Pls help On Thu, Dec 11, 2014 at 8:54 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: the ribbon.mgz isn't part of autorecon2 (or autorecon1) I don't think. What are you trying to run? On Thu, 11 Dec 2014, pradeep mahato wrote: Hi Bruce, After running autorecon1 and autorecon2, I am getting an error saying ribbon.mgz file is missing. Is it that autorecon2 the 23rd function didn't execute. Attaching the recon log also. On Tue, Dec 9, 2014 at 6:48 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Pradeep sorry, I meant autorecon1 and autorecon2 (but not autorecon3) cheers Bruce On Tue, 9 Dec 2014, pradeep mahato wrote: Hi Bruce, I am using Intel Core 2 Quad core processor 2.2 GHz with 4 GB ram. The version i am using is freesurfer-i686-redhat-linux-gnu-stable5-20130513 Using autorecon2 process , I got error saying nu.mgz file is missing. Error : mghRead(/home/nsb/oasis/OAS2_RAW_PART1/OAS1_2/mri/nu.mgz, -1): could not open file Should I include nuintensitycor. Thanks Pradeep On Mon, Dec 8, 2014 at 7:01 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Pradeep you could only run recon-all -autorecon2 instead of -all which should save you some time. 30 hours is pretty long though. What hardware are you using? If you have a modern Linux box with say 4-8 cores it should take less than 10. Or with 2 cores and 4G of ram you could run 2 recons at the same time. What version of FS are you using? The newer ones use openmp, although only the dev version has a bunch of things that take advantage of it. If you want to use more than one core try using -openmmp 4 (to use 4 cores). cheers Bruce On Mon, 8 Dec 2014, pradeep mahato wrote: Hello, I need to extract Hippocampus from brain mri image. The recon-all process takes more than 30 hours to reconstruct from an single image. I am having an dataset of 200 subjects, it is not feasible to run the recon process for all individual brain mri images. Is there any method to possibly get the hippocampus segmented and get the statistical values faster and efficient way. Thanking You Pradeep Kumar Mahato ___ 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. -- Pradeep Kumar Mahato ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Pradeep Kumar Mahato ___ 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. -- Pradeep Kumar Mahato ___ Freesurfer mailing
Re: [Freesurfer] Getting voxel values from aseg.mgz
There is no documentation or example for mri_extract_label. What should be the syntax for it. What kernel and xform file should be used. On Wed, Dec 10, 2014 at 6:50 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Pradeep you can use mri_extract_label to copy just the hippocampal labels out of the segmentation if that is what you mean. The values for left and right hippocampus (17 and 53) can be found in $FREESURFER_HOME/FreeSurferColorLUT.txt cheers Bruce On Wed, 10 Dec 2014, pradeep mahato wrote: After the recon-all process I want to access all the voxels in the left hippocampus ( any subcortical region ) . Please tell me is there any method to extract this voxel values from an segmented image. Thanking you Pradeep Kumar Mahato ___ 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. -- Pradeep Kumar Mahato ___ 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] Getting voxel values from aseg.mgz
After the recon-all process I want to access all the voxels in the left hippocampus ( any subcortical region ) . Please tell me is there any method to extract this voxel values from an segmented image. Thanking you Pradeep Kumar Mahato ___ 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] Best possible atlas to extract hippocampus
Hello, As the complete recon process takes huge time for a single image, is it possible to register the MRI image using a simple atlas. If yes, please explain how to do it. My primary goal is to extract hippocampus in a fastest possible way. Pradeep Kumar Mahato ___ 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] Extracting hippocampus
Hi Bruce, I am using Intel Core 2 Quad core processor 2.2 GHz with 4 GB ram. The version i am using is freesurfer-i686-redhat-linux-gnu-stable5-20130513 Using autorecon2 process , I got error saying nu.mgz file is missing. Error : mghRead(/home/nsb/oasis/OAS2_RAW_PART1/OAS1_2/mri/nu.mgz, -1): could not open file Should I include nuintensitycor. Thanks Pradeep On Mon, Dec 8, 2014 at 7:01 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Pradeep you could only run recon-all -autorecon2 instead of -all which should save you some time. 30 hours is pretty long though. What hardware are you using? If you have a modern Linux box with say 4-8 cores it should take less than 10. Or with 2 cores and 4G of ram you could run 2 recons at the same time. What version of FS are you using? The newer ones use openmp, although only the dev version has a bunch of things that take advantage of it. If you want to use more than one core try using -openmmp 4 (to use 4 cores). cheers Bruce On Mon, 8 Dec 2014, pradeep mahato wrote: Hello, I need to extract Hippocampus from brain mri image. The recon-all process takes more than 30 hours to reconstruct from an single image. I am having an dataset of 200 subjects, it is not feasible to run the recon process for all individual brain mri images. Is there any method to possibly get the hippocampus segmented and get the statistical values faster and efficient way. Thanking You Pradeep Kumar Mahato ___ 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. -- Pradeep Kumar Mahato ___ 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] Extracting hippocampus
Hello, I need to extract Hippocampus from brain mri image. The recon-all process takes more than 30 hours to reconstruct from an single image. I am having an dataset of 200 subjects, it is not feasible to run the recon process for all individual brain mri images. Is there any method to possibly get the hippocampus segmented and get the statistical values faster and efficient way. Thanking You Pradeep Kumar Mahato ___ 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] Cannot allocate memory
Hello All, I get the following error while running mri_glmfit. I am using freesurfer V5.0. But qdce seem to run well with the similar settings. -log--- [pthiyyagura@ fsgd]$ mri_glmfit --glmdir g2v0 --y fsgd_input.mgh --fsgd g2v0.fsgd --C group.diff.mtx gdfReadHeader: reading g2v0.fsgd INFO: gd2mtx_method is dods $Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ cwd /data/rawdata/API/FS_MPRAGE/fsgd cmdline mri_glmfit --glmdir g2v0 --y fsgd_input.mgh --fsgd g2v0.fsgd --C group.diff.mtx sysname Linux hostname machine x86_64 user pthiyyagura FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y/data/rawdata/API/FS_MPRAGE/fsgd/fsgd_input.mgh logyflag 0 usedti 0 FSGD g2v0.fsgd glmdir g2v0 IllCondOK 0 DoFFx 0 Creating output directory g2v0 Loading y from /data/rawdata/API/FS_MPRAGE/fsgd/fsgd_input.mgh MRIalloc: could not allocate 1378828612 slices Cannot allocate memory end--- Any suggestion on this would be greatly appreciated. Thanks, Pradeep ___ 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] Problem while fixing the Surface Topology
Hello Bruce, Thanks for the quick reply. I tried to follow your suggestions, there still seems to be some errors. Hence I am sending you the subject directory, at: http://www.ensc.sfu.ca/~mfbeg/outgoing/topologyCorrectionProblem_PradeepFromSFU.tar.gz When trying to visualize the defect locations, this is what happened. I also tired running the mris_topo_fixer, but it was complaining that there is no lh.qshere. Thanks, Pradeep $ 5:10pm ilpc11: scanner_differences tksurfer FirstOrderPoly lh inflated.nofix surfer: current subjects dir: /ensc/grad1/pkr1/UNSW/scanner_differences surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /ensc/CORTEX/PROJECTS/UNSW/WEIWEN_PARF/PROCESSED_DATA/scanner_differences surfer: Reading header info from /ensc/grad1/pkr1/UNSW/scanner_differences/FirstOrderPoly/mri/T1.mgz surfer: vertices=105340, faces=211208 Loading /ensc/IMAGE_MAIN/SOFTWARE/x86_64/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: using interface /ensc/IMAGE_MAIN/SOFTWARE/x86_64/freesurfer/lib/tcl/tksurfer.tcl Reading /ensc/IMAGE_MAIN/SOFTWARE/x86_64/freesurfer/lib/tcl/tkm_common.tcl Reading /ensc/IMAGE_MAIN/SOFTWARE/x86_64/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /ensc/IMAGE_MAIN/SOFTWARE/x86_64/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /ensc/IMAGE_MAIN/SOFTWARE/x86_64/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... MRISreadVertexPosition(white): could not open file /ensc/grad1/pkr1/UNSW/scanner_differences/FirstOrderPoly/surf/lh.white No such file or directory % alloc: invalid block: 0x13e04e70: 0 0 65 Abort On Mon, Mar 2, 2009 at 4:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Pradeep, sounds like a bug. Can you overlay the surface defect segmentations and see what defect #3 is? If you edit it a bit this will probably go away. If you tar and gzip the subject dir and send it to us we'll take a look You can also try the alternative (newer) topology correction and see if it works properly. Look at the recon-all help for how to run it cheers Bruce On Mon, 2 Mar 2009, Pradeep Reddy Ramana wrote: Hello FS Team, I had a question recently regarding an error encountered in the freesurfer recon-all. I believe error is the result of: mris_fix_topology -mgz -sphere qsphere.nofix -ga FirstOrderPoly lh CORRECTING DEFECT 3 (vertices=10731, convex hull=2557) normal vector of length zero at vertex 90051 with 0 faces vertex 90051 has 0 face No such file or directory recon-all exited with ERRORS I will appreciate very much if you can suggest a possible fix or a rerun with some set of flags etc. The partial log and a previous post by somebody else is here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg09492.html Thanks, Pradeep -- Pradeep Kumar Reddy. Raamana PhD Student - Biomedical Engg. Medical Image Analysis Lab, Simon Fraser University, Burnaby BC - V5A1S6 - Canada. Work : +1 778 782 5509 What is written without effort is, in general, read without pleasure. - Samuel Johnson ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Problem while fixing the Surface Topology
Hello FS Team, I had a question recently regarding an error encountered in the freesurfer recon-all. I believe error is the result of: mris_fix_topology -mgz -sphere qsphere.nofix -ga FirstOrderPoly lh CORRECTING DEFECT 3 (vertices=10731, convex hull=2557) normal vector of length zero at vertex 90051 with 0 faces vertex 90051 has 0 face No such file or directory recon-all exited with ERRORS I will appreciate very much if you can suggest a possible fix or a rerun with some set of flags etc. The partial log and a previous post by somebody else is here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg09492.html Thanks, Pradeep -- Pradeep Kumar Reddy. Raamana PhD Student - Biomedical Engg. Medical Image Analysis Lab, Simon Fraser University, Burnaby BC - V5A1S6 - Canada. Work : +1 778 782 5509 What is written without effort is, in general, read without pleasure. - Samuel Johnson ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Normal vector of length zero
Hello Freesurfer Experts, I ran into the following error when running Freesurfer for one of our subjects, during: mris_fix_topology -mgz -sphere qsphere.nofix -ga FirstOrderPoly lh I could only find a partial answer to a previous post on a similar problem - pasted at the end. Following that, I looked at lh.orig.nofix surface - screenshots attached. I am not sure whether its alright. No rh surfaces were created. Please let me know how to correct this problem and proceed further. Quick response will be greatly appreciated, Pradeep === Tail end of scripts/recon-all.log == # #...@# Fix Topology lh Fri Feb 27 19:29:56 PST 2009 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /ensc/CORTEX/PROJECTS/UNSW/WEIWEN_PARF/PROCESSED_DATA/scanner_differences/FirstOrderPoly/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga FirstOrderPoly lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters * Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations :10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices :0 ordering dependant retessellation: 0 use precomputed edge table :0 smooth retessellated patch :2 match retessellated patch : 1 verbose mode : 0 * INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ $Id: mrisurf.c,v 1.557.2.10 2008/03/10 13:59:45 nicks Exp $ before topology correction, eno=-264 (nv=105340, nf=211208, ne=316812, g=133) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 45195 ambiguous faces found in tessellation segmenting defects... 81 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 6 into 0 -merging segment 7 into 0 -merging segment 0 into 18 -merging segment 39 into 28 -merging segment 37 into 30 -merging segment 54 into 46 -merging segment 53 into 59 -merging segment 72 into 64 -merging segment 71 into 70 72 defects to be corrected 0 vertices coincident reading input surface /ensc/CORTEX/PROJECTS/UNSW/WEIWEN_PARF/PROCESSED_DATA/scanner_differences/FirstOrderPoly/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2008 (-4.6004) -vertex loglikelihood: -6.9827 (-3.4913) -normal dot loglikelihood: -3.5884 (-3.5884) -quad curv loglikelihood: -6.0560 (-3.0280) Total Loglikelihood : -25.8279 CORRECTING DEFECT 0 (vertices=73, convex hull=66) After retessellation of defect 0, euler #=-61 (80515,236855,156279) : difference with theory (-69) = -8 CORRECTING DEFECT 1 (vertices=212, convex hull=29) After retessellation of defect 1, euler #=-60 (80531,236912,156321) : difference with theory (-68) = -8 CORRECTING DEFECT 2 (vertices=14, convex hull=24) After retessellation of defect 2, euler #=-59 (80534,236928,156335) : difference with theory (-67) = -8 CORRECTING DEFECT 3 (vertices=10731, convex hull=2557) normal vector of length zero at vertex 90051 with 0 faces vertex 90051 has 0 face No such file or directory Linux ilpc9.cs.sfu.ca 2.6.18-92.1.22.el5 #1 SMP Tue Dec 16 11:57:43 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Feb 27 21:07:28 PST 2009 -- Previous post with a similar problem --- [Freesurfer] Problem with latest dev version (crashes correcting errors) Tim Jarvis jarv0075 at umn.edu Mon Feb 6 12:41:21 EST 2006 * Previous message: [Freesurfer] Problem with latest dev version (crashes correcting errors) * Next message: [Freesurfer] Problem with latest dev version (crashes correctingerrors) * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] For the lh, there is no cerebellum and no skull, looks to be correct. I don't see any rh* files though? brewster 14% ls /data/brewster2/tjarvis/thesis_data/software/freesurfer/subjects/icbm/surf/ lh.defect_borders
[Freesurfer] Fixing Inaccuracies in White Matter Surfaces
Hello Everybody, This is Pradeep Reddy, just started my PhD in Medical Image Analysis and hence a newbie to FreeSurfer. I've passed the auto-recon2 stage in the reconstruction procedure. Now I am trying to verify WM segmentation produced by the recon-all/auto-recon2, before I move on to further processing. The excercise given in the freesurfer tutorial ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits ) gives me one example on how to detect if there were a lesion and outlines how to fix it. But now when I observe the outputs I have, I am quite confused as to how to detect inaccuracies in the segmentation of white matter. To make it more specific, I show you a slice of wm.mgh I have ( wmConfusion1 attached). Please look at the small yellow circle on the right. If I just follow the exercise, this looks like a lesion, as the yellow line cuts into it. but when I move up to next few slices, this hole opens up ( close to the green line ) giving me indications that it may NOT be a hole ( keeping in mind the inherent 3D nature of the MR image ). Also I am not sure whether there is an error in the image ( wmConfusion5 ) attched is an error is WM segmentation. So my questions: 1. What are the things I have to look for, while trying to verify the WM segmentation ( after autorecon2 )? 2. Any thumb-rules laid out for this already? My googling was in fact in vain. 3. Any other tutorials/resources/books stating clearly what to verify, in different stages of reconstruction? I am sorry to write a long email. Please be kind to help me in this regard. Regards, Pradeep Reddy PhD Student, Simon Fraser Unviersity, Canada. -- There's more to life. Finding it is my job. -- [EMAIL PROTECTED] NOTICE my new contact Number in Canada: +1 604 720 2233 attachment: wmConfusion5-edited.pngattachment: wmConfusion1-edited.png___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
