[Freesurfer] caudate and putamen to surface
Dear all, I want to use caudate and putamen as seed in surface to do PROBTRACK in FSL. For doing that, I acquired target surface which in the cortex seed using kris_convert and label2surf script. But I met some problems in extracting caudate and putamen in the surface. At first I used mdi_extract_label sub1/mri/aseg.auto.noCCseg.mgz 11 /test/L_Caudate.mgz” and it generated L_Caudate.mgz correctly. And then in order to do mri_vol2surf I did bbregister used “bbregister —s sub1 —mov sub1/mri/brain —init-fsl —reg sub1/mri/register.dat”. Then “mdi_vol2surf —src /test/L_Caudate.mgz —srcreg sub1/mri/register.dat —promfrac 0.5 —hemi lh —out /test/L_Caudate2surf.mgz”. Everything looked like went well by the time. But it’s weird when “mri_binarize —i /test/L_Caudate2surf.mgz —min 0.5 —o /test/L_Caudate2surf_bin.mgz” , it showed “Dound 0 values in range” and “Found 0 voxels in final mask”. I checked /test/L_Caudate.mgz and found it was correct. I am wondering is that because of register.dat which I am not very clear how to acquire it correctly? Or is that because lh.white was default used in mri_vol2surf? Could you give me any advises to work around this program? And may be about how to acquire register.dat in this context and how to transform this kind of ROI to surface. Thanks a lot! Sincerely, Jinnan ___ 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] caudate and putamen to surface
Hi Prof. Greve, Thanks for your reply. Sorry, perhaps I have made some mistake in my data analysis. I just want to show tractography results of basal ganglia in surface space using FSL. Could transform fit_paths.nii.gz to surface be a brief way? In order to do mdi_vol2surf (transform volume ROIs in T1 space to surface) I should have register.dat. Is that a correct way to get it using bbregister --s SubID --mov T1.nii --init-fsl --reg register.dat Sincerely, Jinnan ___ 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] Invalid license when run recon-all
Dear FS experts,I want to report an error:I have installed FreeSurfer in my another computer using my license file which works in my old computer. But when I run “recon-all” its shown--ERROR: Invalid FreeSurfer license key found in license file /media/datas/study_tools/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment.—Then,I obtained another license. This error still exists.My environment is : freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /media/datas/study_tools/freesurfer FSFAST_HOME /media/datas/study_tools/freesurfer/fsfast FSF_OUTPUT_FORMATnii.gz SUBJECTS_DIR /media/datas/study_tools/freesurfer/subjects INFO: /home/zhangxx/matlab/startup.m does not exist ... creating MNI_DIR /media/datas/study_tools/freesurfer/mni FSL_DIR /usr/local/fslMy CPU is:Intel Core i5-3470 CPU @ 3.20GHZMy OS is:CentOS 6.5 x64.And log is in the attachment.Please let me know if you have any suggestions!Sincerely，Jinnan recon-all.log Description: Binary data ___ 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 do parcellation in the inflate brain?
Dear FreeSurfer experts, Hello everyone. I am a beginner of Freesurfer. And I want to do parcellation using some templates (are there any accurate templates in surface space?) in the inflate brain after “recon -all” . After that I wish to get some individual areas like M1,SMA and so on in surface space, and then transform then to voxel space. I think it will be more accurate than segment the T1 image in MNI space directly. But unfortunately, after studying for a few weeks I didn’t find a way to do that. So the only way is asking for help…I hope someone could give me some advises or tutorials. If you can help me to solve this problem,I would be very grateful! Sincerely， Jinnan Gong Best wishes for you! Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China ___ 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.
