[Freesurfer] mri_robust_template- Segmentation Fault
Hi there Freesurfer, I am running into a seg fault while running mri_robust_template on freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on a Centos6.2 build. Thinking that this may perhaps be an OS-related issue, I tried to download FS binaries from http://www.freesurfer.net/pub/dist/freesurfer/misc/linux-centos6_x86_64/ but the link is dead Any help would be appreciated Usman $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --satit: Will estimate SAT iteratively! --mov: Using 191_0001.nii.gz as movable/source volume. --mov: Using 192_0001.nii.gz as movable/source volume. Total: 2 input volumes --template: Using test.nii.gz as template output volume. reading source '191_0001.nii.gz'... reading source '192_0001.nii.gz'... Segmentation fault (core dumped) ___ 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] Combining linear transformations
Hi FreeSurfer, I have two images. One MPRAGE (1x1x1mm) and a T1-weighted (0.682x0.682x3mm) image used for CBV mapping. We have run FS, with hippocampal subfields on the MPRAGE and would now like to transform the posterior probability maps to the T1-weighted CBV space. I have been using 1) mri_vol2vol with --regheader to map the posterior_* subfield files to nu.mgz space 2) mri_robust_register to coregister the nu.mgz file to the T1-weighted CBV image Is there any way to combine the .reg and .lta files from (1) and (2) to transform the subfield posterior probability maps directly from their 0.5mm^3 space to the T1-weighted CBV space? I have been reluctant to create an intermediate volume between steps 1 and 2, as resampling the subfield probability maps into 1x1x1mm nu.mgz space will result in loss of resolution to the 0.68x0.68 (coronal) space in the T1-weighted CBV scan. Any help would be appreciated Usman ___ 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] Combining linear transformations
Hi Martin, Thanks for the quick reply. I tried the following commands, but it looks like the volumes are still out of line. Is there something I am missing? to get from hc_subfield --> nu.mgz --> t1_cbv #register and create transforms 1) mri_vol2vol --mov hc_subfield.mgz --targ nu.mgz --reg-final * xfm_hcsubfield_to_nu.dat* --regheader 2) mri_robust_register --mov nu.mgz --dst t1_cbv.mgz --lta *xfm_nu_to_t1.lta * --satit #convert output from (1) from reg-final.dat to .lta 3) tkregister2 --noedit --mov hc_subfield.mgz --targ nu.mgz --reg *xfm_hcsubfield_to_nu.dat --ltaout test.lta* 4) mri_concatenate_lta test.lta xfm_nu_to_t1.lta *final.lta* #apply lta file, using t1_cbv as target and hc_subfield as --mov file 5) mri_vol2vol --mov subfield --targ t1_cbv.mgz --reg *final.lta* --out test.mgz On Tue, Jul 10, 2012 at 6:10 PM, Martin Reuter wrote: > Hi Usman, > > you need to convert the reg to lta (using tkregister2) and then you can > use mri_concatenate_lta . > > Cheers, Martin > > > > On Tue, 2012-07-10 at 17:36 -0400, Usman Khan wrote: > > Hi FreeSurfer, > > I have two images. One MPRAGE (1x1x1mm) and a T1-weighted > > (0.682x0.682x3mm) image used for CBV mapping. We have run FS, with > > hippocampal subfields on the MPRAGE and would now like to transform > > the posterior probability maps to the T1-weighted CBV space. > > > > > > I have been using > > 1) mri_vol2vol with --regheader to map the posterior_* subfield files > > to nu.mgz space > > 2) mri_robust_register to coregister the nu.mgz file to the > > T1-weighted CBV image > > > > > > Is there any way to combine the .reg and .lta files from (1) and (2) > > to transform the subfield posterior probability maps directly from > > their 0.5mm^3 space to the T1-weighted CBV space? I have been > > reluctant to create an intermediate volume between steps 1 and 2, as > > resampling the subfield probability maps into 1x1x1mm nu.mgz space > > will result in loss of resolution to the 0.68x0.68 (coronal) space in > > the T1-weighted CBV scan. > > > > > > Any help would be appreciated > > > > > > Usman > > ___ > > 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] Combining linear transformations
Hi Martin, Thanks for the suggestion. I resolved the issue by using the --regheader flag in tkmregister, and --reg as the default output by mri_vol2vol (even though I did supply a reg-final flag). It seems like I mixed up the difference between reg-final and the default registration matrix. would you mind explaining the difference? in any event, here is my script: for i in $(ls posterior_left_* posterior_Left-Hippocampus.mgz posterior_right_* posterior_Right-Hippocampus.mgz); do fname=$(basename $i); fname=${fname%%.*}; echo "$fname" tkregister2 --noedit --reg hc_subfields/xfm_"$fname".mgz.reg --regheader --targ nu.mgz --mov "$i" --ltaout hc_subfields/xfm_"$fname".lta mri_concatenate_lta hc_subfields/xfm_"$fname".lta xfm_nu_to_pre.lta hc_subfields/xfm_"$fname"_to_pregado.lta mri_convert -at hc_subfields/xfm_"$fname"_to_pregado.lta "$i" hc_subfields/final/final_"$fname".mgz; done Thanks, Usman On Jul 10, 2012, at 10:40 PM, Martin Reuter wrote: Hi Usman , Try validating each step by applying each transform. I usually use mri_convert -at For it. Best Martin Usman Khan wrote: Hi Martin, Thanks for the quick reply. I tried the following commands, but it looks like the volumes are still out of line. Is there something I am missing? to get from hc_subfield --> nu.mgz --> t1_cbv #register and create transforms 1) mri_vol2vol --mov hc_subfield.mgz --targ nu.mgz --reg-final * xfm_hcsubfield_to_nu.dat* --regheader 2) mri_robust_register --mov nu.mgz --dst t1_cbv.mgz --lta *xfm_nu_to_t1.lta * --satit #convert output from (1) from reg-final.dat to .lta 3) tkregister2 --noedit --mov hc_subfield.mgz --targ nu.mgz --reg *xfm_hcsubfield_to_nu.dat --ltaout test.lta* 4) mri_concatenate_lta test.lta xfm_nu_to_t1.lta *final.lta* #apply lta file, using t1_cbv as target and hc_subfield as --mov file 5) mri_vol2vol --mov subfield --targ t1_cbv.mgz --reg *final.lta* --out test.mgz On Tue, Jul 10, 2012 at 6:10 PM, Martin Reuter wrote: > Hi Usman, > > you need to convert the reg to lta (using tkregister2) and then you can > use mri_concatenate_lta . > > Cheers, Martin > > > > On Tue, 2012-07-10 at 17:36 -0400, Usman Khan wrote: > > Hi FreeSurfer, > > I have two images. One MPRAGE (1x1x1mm) and a T1-weighted > > (0.682x0.682x3mm) image used for CBV mapping. We have run FS, with > > hippocampal subfields on the MPRAGE and would now like to transform > > the posterior probability maps to the T1-weighted CBV space. > > > > > > I have been using > > 1) mri_vol2vol with --regheader to map the posterior_* subfield files > > to nu.mgz space > > 2) mri_robust_register to coregister the nu.mgz file to the > > T1-weighted CBV image > > > > > > Is there any way to combine the .reg and .lta files from (1) and (2) > > to transform the subfield posterior probability maps directly from > > their 0.5mm^3 space to the T1-weighted CBV space? I have been > > reluctant to create an intermediate volume between steps 1 and 2, as > > resampling the subfield probability maps into 1x1x1mm nu.mgz space > > will result in loss of resolution to the 0.68x0.68 (coronal) space in > > the T1-weighted CBV scan. > > > > > > Any help would be appreciated > > > > > > Usman > > ___ > > 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] A question about hippocampal subfield segmentation
Hi Lijie (cc to mailing list), I wrote a script to do just this in July. Here is a link to a tar file. It requires knowledge of matlab and bash, but is pretty straight forward. It https://www.dropbox.com/s/s1f78j2ozv1gw8q/subfield_to_ROI.tar.gz a) transforms the subfield probabilities to nu.mgz space (bash, using mri_label2vol) b) applies a threshold to the maps (Koen suggested 50% of max probability, hence 128 of 255) to avoid over-estimation of the subfield volumes (bash) c) comparing the probabilities of individual subfields in IJK space and assigning a unique label to each subfield We can continue this discussion off-line if you like ___ 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.