[Freesurfer] CUDA 9.1 with freesurfer
External Email - Use Caution Dear HCP team , Could you please let me know how i can configure CUDA 9.1 with freesurfer 6.0 or Freesurfer 5.3.0 -HCP It is taking a long time by using openmp to run recon-all. please let me know if you have any suggestions for parallelization. Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] talairach.m3z not found
External Email - Use Caution Dear all, When i run recon-all , i am encountering an error transforms/ talairach.m3z not found during registration phase, could some one please let me know how to resolve this?. Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] How to fasten recon-all execution time without using CUDA
External Email - Use Caution Dear all, I am using - openmp 30 to run recon-all, i see now change in the execution time period. Could you please highlight me a method to reduce the execution time for recon-all, if possible some parallel script to do that same. Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Convert nifti atlas into .annot file
External Email - Use Caution Dear all, How can i create .annot files for both left and right hemisphere from nifti atlases http://www.gin.cnrs.fr/en/tools/aal/ are there any specific guidelines or commands for surface based parcellation ? Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon_all cuda 9.1
External Email - Use Caution Dear, I tried running recon-all -s subjectname -t subjectid -all -openmp 15 , and it still runs very slowly. Is there a faster way to reduce the recon-all time using openmp, please kindly suggest me. Thanks Vasudev On Sat, Aug 31, 2019 at 11:43 AM fsbuild wrote: > Hello Vasudev, > > I think in January of 2018 it was possible to build the development branch > of the freesurfer tree using cuda 5. But I believe that was the last > version we tried building the source with. We no longer support building > with cuda and instead favor using OpenMP. Part of this is because of > cuda’s dependencies on the Nvidia graphics hardware which is a moving > target. Some vendors have essentially stopped supporting Nvidia graphics > card drivers, e.g., Apple as of Mac OS 10.14 onward. The Freesurfer dev > branch source is now compiled with C++ compilers, and I don’t know that > anyone has tried building with cuda since we changed the compilers for > freesurfer. > > - R. > > On Aug 30, 2019, at 11:39, Dev vasu > wrote: > > External Email - Use Caution > > Dear all, > > Does recon_all -use-gpu only works for CUDA 5.0, is there any way to make > it work for CUDA 9.1. > > Thanks > Vasudev > ___ > 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] recon_all cuda 9.1
External Email - Use Caution Dear all, Does recon_all -use-gpu only works for CUDA 5.0, is there any way to make it work for CUDA 9.1. Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Transforming Amygdala nuclei atlas to MNI space
External Email - Use Caution Dear all, I am having a difficulty in transforming the segmented subfields of Amygdala atlas from surface based .mgz to nifti format. I have extracted the labels using mri_extract_label lh.hippoAmygLabels-T1.v21.nii.gz 7009 Cortico_amygloid.mgz then i convert .mgz file to NIFTI using mri_convert Cortico_amygloid.mgz Cortico_amygloid.nii.gz. Later i tried to transform Cortico_amygloid.nii.gz to MNI space using FLIRT but i notice seed region Cortico_amygloid.nii.gz is oriented in different place. Kindly let me know what more i have to do , in order to transform .mgz label into MNI space. Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[WARNING: UNSCANNABLE EXTRACTION FAILED][Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Transforming Amygdala nuclei atlas to MNI space
External Email - Use Caution Dear all, I am having a difficulty in transforming the segmented subfields of Amygdala atlas from surface based .mgz to nifti format. I have extracted the labels using mri_extract_label lh.hippoAmygLabels-T1.v21.nii.gz 7009 Cortico_amygloid.mgz then i convert .mgz file to NIFTI using mri_convert Cortico_amygloid.mgz Cortico_amygloid.nii.gz. Later i tried to transform Cortico_amygloid.nii.gz to MNI space using FLIRT but i notice seed region Cortico_amygloid.nii.gz is oriented in different place. Kindly let me know what more i have to do , in order to transform .mgz label into MNI space. Thanks Vasudev lh.hippoAmygLabels-T1.v21.nii.gz Description: application/gzip cortico_amygloid.nii.gz Description: application/gzip cortico_amygloid.mgz Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert : Error while loading library libGLdispatch.so.0
External Email - Use Caution Dear all, I am trying to convert .mgz file to nii.gz using mri_convert command mri_convert filename.mgz filename.nii.gz but i am getting an error "mri_convert: error while loading shared libraries: libGLdispatch.so.0: cannot open shared object file: No such file or directory " Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Thalamic Nuclei segmentation results
External Email - Use Caution Dear all, I have used Freesurfer pipeline for Thalamic Nuclei segmentation, the results of segmentation appear to be very poor, i am annexing the results , please kindly review if there is any thing wrong with the segmentation results. Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all -make all error
External Email - Use Caution Dear all, I am encountering following error whenever i re-rerun my recon-all on cluster,,although i have downloaded new development version of recon-all.makefile, this error persists,kindly let me know what i am doing wrong recon-all -make all -s /home/hpc/u7x32/ru37veh2/emilie_struc/HC13 -sd /home/hpc/u7x32/ru37veh2/emilie_struc/new_recon -- recon-all -make all -s /home/hpc/u7x32/ru37veh2/emilie_struc/HC13 -sd /home/hpc/u7x32/ru37veh2/emilie_struc/new_recon /home/hpc/u7x32/ru37veh2/freesurfer_dev/bin/recon-all.makefile:195: recipe for target '/home/hpc/u7x32/ru37veh2/emilie_struc/new_recon/HC13/surf/lh.white.preaparc' failed recon-all -make all -s /home/hpc/u7x32/ru37veh2/emilie_struc/HC13 -sd /home/hpc/u7x32/ru37veh2/emilie_struc/new_reconmake: *** [/home/hpc/u7x32/ru37veh2/emilie_struc/new_recon/HC13/surf/lh.white.preaparc] Error 1 Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all terminated in middle : continuing an analysis of an existing subject
External Email - Use Caution Dear all, I was trying to run recon-all, the pipeline terminated in middle now i would like to know if there is any way i can restart it from the point where it was terminated?. Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas
External Email - Use Caution Dear All, I have a problem with the Freesurfer hippocampal longitudinal segmentation results , when i have done segmentation using following algorithm ( https://github.com/CobraLab/antsRegistration-MAGeT) with no anterior/posterior partitioning ( Head/body/tail ) , on my subject pool the volumes that i have obtained for each subfield is very different from the volumes of corresponding subfields that i am getting when i have done subfield segmentation using freesurfer. I think algorithm does influence the segmentation procedure, if this is the case then i am getting different results for histology based segmentation using https://github.com/CobraLab/antsRegistration-MAGeT and freesurfer. When i compare the subfield volumes between healthy and disease patients that i have obtained using first segmentation procedure using ANTS-MAGeT , i notice statistical significance in subfields like CA1,CA2-CA3 but when i do the same using freesurfer based algorithm i notice no statistical significance in these subfields. Do you think the algorithm has any influence on segmentation to such a level that we get completely different results on two occasions. Thanks Vasudev ___ 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] Problems associated segmentation results of hippocampal subfields
External Email - Use Caution Dear All, I have a problem with the Freesurfer hippocampal longitudinal segmentation results , when i have done segmentation using following algorithm ( https://github.com/CobraLab/antsRegistration-MAGeT) with no anterior/posterior partitioning ( Head/body/tail ) , on my subject pool the volumes that i have obtained for each subfield is very different from the volumes of corresponding subfields that i am getting when i have done subfield segmentation using freesurfer. I think algorithm does influence the segmentation procedure, if this is the case then i am getting different results for histology based segmentation using https://github.com/CobraLab/antsRegistration-MAGeT and freesurfer. When i compare the subfield volumes between healthy and disease patients that i have obtained using first segmentation procedure using ANTS-MAGeT , i notice statistical significance in subfields like CA1,CA2-CA3 but when i do the same using freesurfer based algorithm i notice no statistical significance in these subfields. Do you think the algorithm has any influence on segmentation to such a level that we get completely different results on two occasions. Thanks Vasudev ___ 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] Anterior / Posterior Partition in Hippocampus parcellation atlas
External Email - Use Caution Dear Sir, I was able to generate segmentations as cited in the module , I am able obtain segmentations for CA1 posterior Head and CA1 Posterior body , along with CA1 head and CA1 body , what does non posterior parcellations of CA1 head and body indicates, can these be assumed as anterior regions ?, is there any way to obtain CA1 head and CA1 body etc for both left and right hemispheres , as per segmentation results i can only see *[lr]h.hippoSfVolumes-T1.v2x.mgz files * . Not (lr)h.CA1_head and body , how can i split these subfields from *[lr]h.hippoSfVolumes-T1.v2x.mgz files.* *Thanks* *Vasudev* On Tue, Jul 3, 2018 at 11:49 AM, Iglesias Gonzalez, Eugenio < e.igles...@ucl.ac.uk> wrote: > Yes! > > > Juan Eugenio Iglesias > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > -- > *From:* Dev vasu > *Sent:* Tuesday, July 3, 2018 12:22:27 AM > *To:* Iglesias Gonzalez, Eugenio > *Cc:* freesurfer@nmr.mgh.harvard.edu > > *Subject:* Re: Anterior / Posterior Partition in Hippocampus parcellation > atlas > > Dear Sir, > > I have another query if i use "export WRITE_POSTERIORS=1", will it > generate posterior CA1 and other substructures in the form as cited > *posterior_sidev2x.mgz > , * > > > Thanks > Vasudev > > On Mon, Jul 2, 2018 at 8:30 PM, Dev vasu gmail.com> wrote: > > Dear Sir, > > Thanks for your reply Yes,i have run 6.0, Can you send me the link for > developmental version of freesurfer, also how can i obtain posterior > regions of subfields like CA1,CA2,CA3,CA4, as the link suggests only CA1 > head and CA1 body were segmented , i need posterior part of CA1 can i > assume CA1 body as posterior region. > > > Thanks > Vasudev > > On Mon, Jul 2, 2018 at 8:25 PM, Iglesias Gonzalez, Eugenio < > e.igles...@ucl.ac.uk> wrote: > > Ah, now I understand. > > To get the division in the wiki (https://surfer.nmr.mgh.harvar > d.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala), you need to run > the development version of FreeSurfer. The version you ran (6.0, I > presume), does not provide such subdivision. > > In principle, you could use Garikoitz’s code to subdivide the > segmentation, but his code is not part of FreeSurfer, so you would have to > contact him for support. Alternatively, you can also download the > development version of FreeSurfer, which will provide the segmentation that > I mentioned earlier. > > Kind regards, > > /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: *Dev vasu > *Date: *Monday, 2 July 2018 at 19:22 > *To: *"Iglesias Gonzalez, Eugenio" > *Cc: *"freesurfer@nmr.mgh.harvard.edu" , " > igles...@nmr.mgh.harvard.edu" > *Subject: *Re: Anterior / Posterior Partition in Hippocampus parcellation > atlas > > > > Dear sir, > > > > In the following journal published by you ,procedure for longitudinal > segmentation was highlighted (https://github.com/garikoitz/hippovol) , I > have run the module described in wiki and i have obtained > lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz and lh.hippoSfLabels-T1.v10.mgz > files , i would like to know how i can split the labels CA1 head, CA1 body > and CA1 tail from this file, since individual subfield label numbers for > CA1 head and CA1 body are not defined ,also can i assure CA1 body as > posterior region and CA1 head as anterior ?. > > > > > > Thanks > > Vasudev > > > > On Mon, Jul 2, 2018 at 7:39 PM, Iglesias Gonzalez, Eugenio < > e.igles...@ucl.ac.uk> wrote: > > Dear Vasudev, > > You can run the module described in that wiki page, and in the output file > [lr]h.hippoAmygLabels-T1.v2x.mgz you will find segmentations for CA1 > head, CA1 body, CA23 head, CA23 body, CA4 head, CA4 body, and hippocampal > tail (note that we don’t parcellate the tail). > > 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: *Dev vasu > *Date: *Monday, 2 July 2018 at 17:09 > *To: *"freesurfer@nmr.mgh.harvard.edu" , " > igles...@nmr.mgh.harvard.edu" > *Subject: *Anterior /
Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas
External Email - Use Caution Dear Sir, I have another query if i use "export WRITE_POSTERIORS=1", will it generate posterior CA1 and other substructures in the form as cited *posterior_sidev2x.mgz , * Thanks Vasudev On Mon, Jul 2, 2018 at 8:30 PM, Dev vasu < vasudevamurthy.devulapa...@gmail.com> wrote: > Dear Sir, > > Thanks for your reply Yes,i have run 6.0, Can you send me the link for > developmental version of freesurfer, also how can i obtain posterior > regions of subfields like CA1,CA2,CA3,CA4, as the link suggests only CA1 > head and CA1 body were segmented , i need posterior part of CA1 can i > assume CA1 body as posterior region. > > > Thanks > Vasudev > > On Mon, Jul 2, 2018 at 8:25 PM, Iglesias Gonzalez, Eugenio < > e.igles...@ucl.ac.uk> wrote: > >> Ah, now I understand. >> >> To get the division in the wiki (https://surfer.nmr.mgh.harvar >> d.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala), you need to run >> the development version of FreeSurfer. The version you ran (6.0, I >> presume), does not provide such subdivision. >> >> In principle, you could use Garikoitz’s code to subdivide the >> segmentation, but his code is not part of FreeSurfer, so you would have to >> contact him for support. Alternatively, you can also download the >> development version of FreeSurfer, which will provide the segmentation that >> I mentioned earlier. >> >> Kind regards, >> >> /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: *Dev vasu >> *Date: *Monday, 2 July 2018 at 19:22 >> *To: *"Iglesias Gonzalez, Eugenio" >> *Cc: *"freesurfer@nmr.mgh.harvard.edu" , >> "igles...@nmr.mgh.harvard.edu" >> *Subject: *Re: Anterior / Posterior Partition in Hippocampus >> parcellation atlas >> >> >> >> Dear sir, >> >> >> >> In the following journal published by you ,procedure for longitudinal >> segmentation was highlighted (https://github.com/garikoitz/hippovol) , I >> have run the module described in wiki and i have obtained >> lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz and lh.hippoSfLabels-T1.v10.mgz >> files , i would like to know how i can split the labels CA1 head, CA1 body >> and CA1 tail from this file, since individual subfield label numbers for >> CA1 head and CA1 body are not defined ,also can i assure CA1 body as >> posterior region and CA1 head as anterior ?. >> >> >> >> >> >> Thanks >> >> Vasudev >> >> >> >> On Mon, Jul 2, 2018 at 7:39 PM, Iglesias Gonzalez, Eugenio < >> e.igles...@ucl.ac.uk> wrote: >> >> Dear Vasudev, >> >> You can run the module described in that wiki page, and in the output >> file [lr]h.hippoAmygLabels-T1.v2x.mgz you will find segmentations for >> CA1 head, CA1 body, CA23 head, CA23 body, CA4 head, CA4 body, and >> hippocampal tail (note that we don’t parcellate the tail). >> >> 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: *Dev vasu >> *Date: *Monday, 2 July 2018 at 17:09 >> *To: *"freesurfer@nmr.mgh.harvard.edu" , >> "igles...@nmr.mgh.harvard.edu" >> *Subject: *Anterior / Posterior Partition in Hippocampus parcellation >> atlas >> >> >> >> *External Email - Use Caution* >> >> Dear Sir, >> >> >> >> >> >> I have reviewed your journal which detailed about hippocampus >> parcellation ( https://surfer.nmr.mgh.harvard >> .edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala ) of subfields ( HBT >> - Head/body/Tail) , could you please let me know how to partition the atlas >> along the lines of Anterior CA1,CA3,CA4 and posterior CA1,CA3,CA4. >> >> >> >> >> >> Thanks >> >> Vasdudev >> >> 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] Anterior / Posterior Partition in Hippocampus parcellation atlas
External Email - Use Caution Dear Sir, Thanks for your reply Yes,i have run 6.0, Can you send me the link for developmental version of freesurfer, also how can i obtain posterior regions of subfields like CA1,CA2,CA3,CA4, as the link suggests only CA1 head and CA1 body were segmented , i need posterior part of CA1 can i assume CA1 body as posterior region. Thanks Vasudev On Mon, Jul 2, 2018 at 8:25 PM, Iglesias Gonzalez, Eugenio < e.igles...@ucl.ac.uk> wrote: > Ah, now I understand. > > To get the division in the wiki (https://surfer.nmr.mgh. > harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala), you need to > run the development version of FreeSurfer. The version you ran (6.0, I > presume), does not provide such subdivision. > > In principle, you could use Garikoitz’s code to subdivide the > segmentation, but his code is not part of FreeSurfer, so you would have to > contact him for support. Alternatively, you can also download the > development version of FreeSurfer, which will provide the segmentation that > I mentioned earlier. > > Kind regards, > > /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: *Dev vasu > *Date: *Monday, 2 July 2018 at 19:22 > *To: *"Iglesias Gonzalez, Eugenio" > *Cc: *"freesurfer@nmr.mgh.harvard.edu" , " > igles...@nmr.mgh.harvard.edu" > *Subject: *Re: Anterior / Posterior Partition in Hippocampus parcellation > atlas > > > > Dear sir, > > > > In the following journal published by you ,procedure for longitudinal > segmentation was highlighted (https://github.com/garikoitz/hippovol) , I > have run the module described in wiki and i have obtained > lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz and lh.hippoSfLabels-T1.v10.mgz > files , i would like to know how i can split the labels CA1 head, CA1 body > and CA1 tail from this file, since individual subfield label numbers for > CA1 head and CA1 body are not defined ,also can i assure CA1 body as > posterior region and CA1 head as anterior ?. > > > > > > Thanks > > Vasudev > > > > On Mon, Jul 2, 2018 at 7:39 PM, Iglesias Gonzalez, Eugenio < > e.igles...@ucl.ac.uk> wrote: > > Dear Vasudev, > > You can run the module described in that wiki page, and in the output file > [lr]h.hippoAmygLabels-T1.v2x.mgz you will find segmentations for CA1 > head, CA1 body, CA23 head, CA23 body, CA4 head, CA4 body, and hippocampal > tail (note that we don’t parcellate the tail). > > 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: *Dev vasu > *Date: *Monday, 2 July 2018 at 17:09 > *To: *"freesurfer@nmr.mgh.harvard.edu" , " > igles...@nmr.mgh.harvard.edu" > *Subject: *Anterior / Posterior Partition in Hippocampus parcellation > atlas > > > > *External Email - Use Caution* > > Dear Sir, > > > > > > I have reviewed your journal which detailed about hippocampus parcellation > ( https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiO > fAmygdala ) of subfields ( HBT - Head/body/Tail) , could you please let > me know how to partition the atlas along the lines of Anterior CA1,CA3,CA4 > and posterior CA1,CA3,CA4. > > > > > > Thanks > > Vasdudev > > 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] Anterior / Posterior Partition in Hippocampus parcellation atlas
External Email - Use Caution Dear sir, In the following journal published by you ,procedure for longitudinal segmentation was highlighted (https://github.com/garikoitz/hippovol) , I have run the module described in wiki and i have obtained lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz and lh.hippoSfLabels-T1.v10.mgz files , i would like to know how i can split the labels CA1 head, CA1 body and CA1 tail from this file, since individual subfield label numbers for CA1 head and CA1 body are not defined ,also can i assure CA1 body as posterior region and CA1 head as anterior ?. Thanks Vasudev On Mon, Jul 2, 2018 at 7:39 PM, Iglesias Gonzalez, Eugenio < e.igles...@ucl.ac.uk> wrote: > Dear Vasudev, > > You can run the module described in that wiki page, and in the output file > [lr]h.hippoAmygLabels-T1.v2x.mgz you will find segmentations for CA1 > head, CA1 body, CA23 head, CA23 body, CA4 head, CA4 body, and hippocampal > tail (note that we don’t parcellate the tail). > > 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: *Dev vasu > *Date: *Monday, 2 July 2018 at 17:09 > *To: *"freesurfer@nmr.mgh.harvard.edu" , " > igles...@nmr.mgh.harvard.edu" > *Subject: *Anterior / Posterior Partition in Hippocampus parcellation > atlas > > > > *External Email - Use Caution* > > Dear Sir, > > > > > > I have reviewed your journal which detailed about hippocampus parcellation > ( https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiO > fAmygdala ) of subfields ( HBT - Head/body/Tail) , could you please let > me know how to partition the atlas along the lines of Anterior CA1,CA3,CA4 > and posterior CA1,CA3,CA4. > > > > > > Thanks > > Vasdudev > > 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] Anterior / Posterior Partition in Hippocampus parcellation atlas
External Email - Use Caution Dear Sir, I have reviewed your journal which detailed about hippocampus parcellation ( https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala ) of subfields ( HBT - Head/body/Tail) , could you please let me know how to partition the atlas along the lines of Anterior CA1,CA3,CA4 and posterior CA1,CA3,CA4. Thanks Vasdudev ___ 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] How to obtain a label for Custom ROI mask
Dear all, I have custom ROI mask ( MNI Space ) that i have prepared from Jülich atlas , I would be like to obtain corresponding surface label file, Could you please guide me necessary the steps that i have to follow inorder to obtain corresponding label for my mask. Thanks Vasudev ___ 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] Generating Mean thickness surface file for volume ROI mask
Dear all, I have a ROI mask volume file and i would like to generate Mean cortical thickness surface file (i.e lh.ROI.thickness.fsaverage.mgh and rh.ROI.thickness.fsaverage.mgh) , could some one guide me how i could obtain such file. I have 120 subjects and I have done recon-all for all subjects. Thanks Vasudev ___ 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] Cortical Thickness of Hippocampus subfields
Dear Sir, I have performed Subfield segmentation of Hippocampus subfields, I would like to how i can calculate thickness of each subfield post segmentation, are the values in the text files *[lr]h.hippoSfVolumes--.v10.txt*: indicate estimated volume of each subfield , Is there any way i can obtain thickness of each subfield w.r.t whole hippocampus ?. Thanks Vasudev ___ 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] Hippocampus subfield segmentation Aborted
Dear all,
I am encountering following error when i run Hippocampus subfield
segmentation
"run_segmentSubjectT1_autoEstimateAlveusML.sh: line 46: 11266
Aborted "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML
$args ".
I am annexing the log file for your notice please kindly review it and let
me know why its getting intermittently aborted .
Thanks
Vasudev
#
#@# Hippocampal Subfields processing (T1 only) left Fri Jul 21 13:57:20 EDT 2017
--
Setting up environment variables
---
LD_LIBRARY_PATH is .:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/runtime/glnxa64:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/bin/glnxa64:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/os/glnxa64:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/project/m/mchakrav/quarantine/ANTs/git/build/lib:/scinet/gpc/Libraries/zlib-1.2.8/lib:/scinet/gpc/tools/Python/Python272-shared/lib:/scinet/gpc/intel/compilers_and_libraries_2016.3.210/linux/ipp/lib/intel64:/scinet/gpc/intel/compilers_and_libraries_2016.3.210/linux/tbb/lib/intel64:/scinet/gpc/compilers/gcc-5.2.0/requiredlibs/lib:/scinet/gpc/compilers/gcc-5.2.0/lib:/scinet/gpc/compilers/gcc-5.2.0/lib64:/scinet/gpc/lib64_6.4:/scinet/gpc/lib64_6.4/mysql:/scinet/gpc/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64:/scinet/gpc/intel/debugger_2016/libipt/intel64/lib:/scinet/gpc/intel/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64
terminate called after throwing an instance of 'std::runtime_error'
what(): locale::facet::_S_create_c_locale name not valid
/sgfs1/scratch3/m/mchakrav/vasudev/freesurfer/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 46: 11266 Aborted "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args
#
#@# Hippocampal Subfields processing (T1 only) right Fri Jul 21 13:57:20 EDT 2017
--
Setting up environment variables
---
LD_LIBRARY_PATH is .:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/runtime/glnxa64:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/bin/glnxa64:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/os/glnxa64:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/scratch/m/mchakrav/vasudev/freesurfer/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/project/m/mchakrav/quarantine/ANTs/git/build/lib:/scinet/gpc/Libraries/zlib-1.2.8/lib:/scinet/gpc/tools/Python/Python272-shared/lib:/scinet/gpc/intel/compilers_and_libraries_2016.3.210/linux/ipp/lib/intel64:/scinet/gpc/intel/compilers_and_libraries_2016.3.210/linux/tbb/lib/intel64:/scinet/gpc/compilers/gcc-5.2.0/requiredlibs/lib:/scinet/gpc/compilers/gcc-5.2.0/lib:/scinet/gpc/compilers/gcc-5.2.0/lib64:/scinet/gpc/lib64_6.4:/scinet/gpc/lib64_6.4/mysql:/scinet/gpc/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64:/scinet/gpc/intel/debugger_2016/libipt/intel64/lib:/scinet/gpc/intel/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64
terminate called after throwing an instance of 'std::runtime_error'
what(): locale::facet::_S_create_c_locale name not valid
/sgfs1/scratch3/m/mchakrav/vasudev/freesurfer/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 46: 11332 Aborted "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args
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[Freesurfer] mri_concat to perform average cortical thickness & pial surface
Dear all, I have 115 subjects , and I would like to perform average cortical thickness ,pial surface . I have used mri_concat for this and i am getting dimension mismatch *" mri_concat k***/surf/lh.thickness --mean --o /media/vasudev/vkirsch4/Data_Driven/Thickness_Pial/lh_thickness/lh.thickness.fsaverage.mean.mgh ninputs = 115Checking inputsERROR: dimension mismatch between k100/surf/lh.thickness and k102/surf/lh.thickness "* I have checked the dimensions of the subjects and following is the output , it seems there is a problem with dimensions of all the thickness files, could some one please let me know how i could perform group average thickness in this case ? " mri_info k102/surf/lh.thickness Volume information for k102/surf/lh.thickness type: curv dimensions: 109303 x 1 x 1 voxel sizes: 1., 1., 1. type: FLOAT (3) fov: 109303.000 dof: 0 xstart: -54651.5, xend: 54651.5 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform not present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 0. : x_a = 0., y_a = 0., z_a = 1., c_a = 0. : x_s = 0., y_s = -1., z_s = 0., c_s = 0. Orientation : ??? Primary Slice Direction: unknown voxel to ras transform: -1. 0. 0. 54651.5000 0. 0. 1.-0.5000 0. -1. 0. 0.5000 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. 0. 0. 54651.5000 -0. -0. -1. 0.5000 -0. 1. -0. 0.5000 0. 0. 0. 1. " mri_info k100/surf/lh.thickness Volume information for k100/surf/lh.thickness type: curv dimensions: 116434 x 1 x 1 voxel sizes: 1., 1., 1. type: FLOAT (3) fov: 116434.000 dof: 0 xstart: -58217.0, xend: 58217.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform not present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 0. : x_a = 0., y_a = 0., z_a = 1., c_a = 0. : x_s = 0., y_s = -1., z_s = 0., c_s = 0. Orientation : ??? Primary Slice Direction: unknown voxel to ras transform: -1. 0. 0. 58217. 0. 0. 1.-0.5000 0. -1. 0. 0.5000 0. 0. 0. 1. " Thanks, Vasudev ___ 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] [FSL] Re Orient image from AP to PA axis
Dear all, I would like to if there is any procedure to reorient the image ( flip ) from AP axis to PA , I have around 50 scans all of which are scanned in A/P axis and i would like to reorient them , kindly please let me know if there is any procedure. I tried mri_convert and orient_mri is freesurfer but i could not see any changes Thanks Vasudev ___ 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] lh.white.H , Failed to create
Dear all , I have been incurring lot of problems while running recon-all on ubuntu 16.04 , recon-all throws following error : " #@# Curv .H and .K lh Sa 25. Feb 04:09:16 CET 2017 /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/surf mris_curvature -w lh.white.preaparc total integrated curvature = 8.913*4pi (112.005) --> -8 handles ICI = 172.8, FI = 1966.7, variation=30317.492 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H ln: failed to create symbolic link 'lh.white.H': Function not implemented " Could you please let me know why this error is occurring . Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Talairach Registration Error : recon-all -s
Dear FreeSurfer Developers, I am incurring Talairach registration error when i was running recon-all -s Error : recon-all -s KON2 exited with ERRORS at Do 16. Feb 16:23:10 CET 2017 Freesurfer Version : freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP Platform: Ubuntu 16.04 recon-all log : see the attachment Kindly let me know the problem with registration. Thanks, Vasudev Do 16. Feb 16:22:48 CET 2017 /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2 /usr/local/bin/freesurfer/bin/recon-all -i /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/T1w_acpc_dc_restore_1mm.nii.gz -subjid KON2 -sd /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w -motioncor -talairach -nuintensitycor -normalization subjid KON2 setenv SUBJECTS_DIR /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w FREESURFER_HOME /usr/local/bin/freesurfer Actual FREESURFER_HOME /usr/local/bin/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP Linux vasudev-OptiPlex-780 4.4.0-62-generic #83-Ubuntu SMP Wed Jan 18 14:10:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 59733 maxlocks unlimited maxsignal59733 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited totalusedfree shared buff/cache available Mem: 15332320 2811540 4498076 194844 802270411938640 Swap: 0 0 0 program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-15:22:48-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-15:22:48-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-15:22:48-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-15:22:49-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-15:22:49-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-15:22:49-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-15:22:49-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: vasudev Machine: vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-15:22:49-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: vasudev Machine: vasudev-Opti
[Freesurfer] Cortical thickness changes in Hippocampus sub fields
Dear all, I would like to perform Group ROI analysis between healthy controls and BVF patients where i would like measure cortical thickness changes between healthy controls and BVF, what changes should i adopt to my initial preprocessing tasks using recon-all in order to evaluate changes in cortical thickness and possibly sulcal depth. Any suggestions are greatly appreciated . Thanks VAsudev ___ 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] Surface based analysis for hippocampus subfield thickness
Dear all, Is there any approach that you recommend to quantify that changes in cortical thickness in hippo campus sub fields , how could i perform Surface based cortical thickness changes using freesurfer. Thanks Vasudev ___ 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] Converstion of Wavefront .obj files into Nifti
Dear all, Could you please suggest me some method where i can possibly convert Wavefront .obj files into Nifti files, is such conversion technically relevant ?. Thanks Vasudev ___ 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] Group analysis Cortical Thickness
Dear Freesurfer Group, I would like to perform group analysis for 50 Subjects (25 healthy controls and 25 Subjects with BLVP ) and examine the changes in cortical thickness between 2 groups, could you please kindly inform me some methods that i should adapt to perform the analysis. Thanks Vasudev ___ 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] Calculating IntraCranial Volume (ICV) for multiple subjects
Dear all, I would like to like obtain the data values of IntraCranial Volume (ICV) for 10 subjects , i know that recon-all automatically calls mri_segstats, but i would like to know if there is any other method to obtain ICV quickly, since running recon-all on each subject takes a lot of time. Thanks Vasudev ___ 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] Calculating IntraCranial Volume (ICV) for multiple subjects
Dear all, I would like to like obtain the data values of IntraCranial Volume (ICV) for 10 subjects , i know that recon-all automatically calls mri_segstats, but i would like to know if there is any other method to obtain ICV quickly, since running recon-all on each subject takes a lot of time. Thanks Vasudev ___ 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] Recon-all GNU parallel Error. : Segmentation fault
Dear Sir / madam,
I have tried running recon-all with GNU parallel and i am incurring
following error kindly review the recon-all.log ( see below ).
Could you please let me know why such problem persists for me. Is it the
issue with memory space ?
Thanks
Vasudev
Calling the GNU parallel in terminal
" ls PAT*.nii.gz | sed 's/.nii.gz//' | parallel --jobs 5 recon-all -s {} -i
{}.nii.gz -all -qcache "
recon-all-log
Fr 2. Sep 17:59:48 CEST 2016
/media/vasudev/Daten/VBCT_results/PAT30
/usr/local/bin/freesurfer/bin/recon-all
-s PAT30 -i PAT30.nii.gz -all -qcache
subjid PAT30
setenv SUBJECTS_DIR /media/vasudev/Daten/VBCT_results
FREESURFER_HOME /usr/local/bin/freesurfer
Actual FREESURFER_HOME /usr/local/bin/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP
Linux vasudev-OptiPlex-780 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun
29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 15208
maxlocks unlimited
maxsignal15208
maxmessage 819200
maxnice 0
maxrtprio0
maxrttimeunlimited
total used free sharedbuffers cached
Mem: 39154323730516 184916 17476 21512 505448
-/+ buffers/cache:3203556 711876
Swap:0 0 0
program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva
(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
###
GCADIR /usr/local/bin/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /usr/local/bin/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
###
/media/vasudev/Daten/VBCT_results/PAT30
mri_convert /media/vasudev/Daten/VBCT/PAT30.nii.gz
/media/vasudev/Daten/VBCT_results/PAT30/mri/orig/001.mgz
Linux vasudev-OptiPlex-780 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun
29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s PAT30 exited with ERRORS at Fr 2. Sep 17:59:56 CEST 2016
To report a problem, see http://surfer.nmr.mgh.harvard.
edu/fswiki/BugReporting
___
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] Recon-all GNU parallel Error. : Segmentation fault
Dear Sir / madam,
I have tried running recon-all with GNU parallel and i am incurring
following error kindly review the recon-all.log ( see below ).
Could you please let me know why such problem persists for me. Is it the
issue with memory space ?
Thanks
Vasudev
Calling the GNU parallel in terminal
" ls PAT*.nii.gz | sed 's/.nii.gz//' | parallel --jobs 5 recon-all -s {} -i
{}.nii.gz -all -qcache "
recon-all-log
Fr 2. Sep 17:59:48 CEST 2016
/media/vasudev/Daten/VBCT_results/PAT30
/usr/local/bin/freesurfer/bin/recon-all
-s PAT30 -i PAT30.nii.gz -all -qcache
subjid PAT30
setenv SUBJECTS_DIR /media/vasudev/Daten/VBCT_results
FREESURFER_HOME /usr/local/bin/freesurfer
Actual FREESURFER_HOME /usr/local/bin/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP
Linux vasudev-OptiPlex-780 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun
29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 15208
maxlocks unlimited
maxsignal15208
maxmessage 819200
maxnice 0
maxrtprio0
maxrttimeunlimited
total used free sharedbuffers cached
Mem: 39154323730516 184916 17476 21512 505448
-/+ buffers/cache:3203556 711876
Swap:0 0 0
program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva
(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
###
GCADIR /usr/local/bin/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /usr/local/bin/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
###
/media/vasudev/Daten/VBCT_results/PAT30
mri_convert /media/vasudev/Daten/VBCT/PAT30.nii.gz
/media/vasudev/Daten/VBCT_results/PAT30/mri/orig/001.mgz
Linux vasudev-OptiPlex-780 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun
29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s PAT30 exited with ERRORS at Fr 2. Sep 17:59:56 CEST 2016
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
___
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] rfMRI and T2w image
Dear sir, I was checking for your reply about my question in Freesurfer Forum but unfortunately i could not your answer although ":Freesurfer Digest, Vol 150, Issue 43 " Today's topics section indicates that you have replied to my question. Following is my question : In order to run my structural analysis pipeline , i require T2w images, but unfortunately we have not performed T2w scans , my colleague suggests we can use rfMRI instead T2w images Could you please let me know if i can use rfMRI image instead of T2w image?. Thanks Vasudev ___ 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] rfMRI and T2w image
Dear Sir, In order to run my structural analysis pipeline , i require T2w images, but unfortunately we have not performed T2w scans , my colleague suggests we can use rfMRI instead T2w images Could you please let me know if i can use rfMRI image instead of T2w image?. Thanks Vasudev ___ 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] wmparc parcellation for thalamus and brainstem
Dear all, After running through recon-all ,I have obtained wmparc parcellation file (see the attached figure ). I would like to obtain parcellation at specific regions of interest for my study i.e Brain stem region and Thalamus region, could you please let me know how i could perform parcellation for these two specific regions of interest ( i.e. Brain stem and Thalamus ). Thanks Vasudev ___ 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] Obtaining White and pial surface maps for multiple subjects
Dear sir, I would like to know how could i possibly generate white and pial surface data for pool of 50 subjects ( 25 healthy controls and 2 subjects with BLVP) using free surfer. Thanks Vasudev ___ 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] Measuring cortical thickness
Dear Sir / madam, I have 50 subjects (25 healthy controls and 25 patients with BLVP) , I would like to know how could i generate cortical thickness maps for multi subject group analysis. The initial pre-processing with recon-all takes several hours for single subject, is there any alternate way to approach this problem in a limited amount of time?. Any help would be greatly appreciated. Thanks Vasudev ___ 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.
