Freesurfer

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30132 discussions

DKT40 classifier atlas
by Yixin Ma 22 Jan '19

22 Jan '19

External Email - Use Caution Hi Freesurfer experts, I'm writing to ask how can I reconstruct the DKT40 classifier atlas. Is it included in recon -all? Thank you for your help. Best regards, Yixin Ma

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how to register feature maps to fsaverage6?
by 310913949 22 Jan '19

22 Jan '19

External Email - Use Caution Dear freesurfer experts： I want to know how to register feature maps to an average space (fsaverage6) so that I can get an identical number of vertices(40962) for each hemisphere. Can you tell me what is the command line? I am looking forward to your reply!Thanks. ------------------ 邓刊 Kan Deng E-mail：310913949(a)qq.com TEL：13728774014

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Re: [Freesurfer] Tracula: Transform streamlines to T1 RAS coordinates
by Yendiki, Anastasia 22 Jan '19

22 Jan '19

Hi Donald - Both your input and output reference volume are in diffusion space and there is no transformation specified, so the output is also in diffusion space. These are voxel, not RAS, coordinates. Best, a.y On Jan 22, 2019 7:14 AM, "Krieger, Donald N." <kriegerd(a)upmc.edu> wrote: External Email - Use Caution I extract the streamlines for each tract from path.pd.trk to an ascii file and then wish to transform the coordinates to RAS T1 coordinates in millimeters. My results are not correct. Here is the extraction command I’m using. Is this correct? Perhaps I should be using orig.mgz as the outref volume? I do not understand –inref and --outref dmri_trk2trk –in path.pd.trk –inref path.pd.nii.gz –outref path.pd.nii.gz –outasc test.streamlines Given the above command, I am assuming that the output I’m getting is in the diffusion frame in voxel coordinates. I extract 4x4 transforms and apply them in sequence; I append 1.0 to each 3-vector before applying them of course. Here is the most compact approach I’ve tried 1st transform: mri_info –in path.pd.nii.gz –vox2ras-tkr 2nd transform: mri_info –in orig.mgz –tkr2scanner I’ve also tried this: 1st transform: mri_info –in path.pd.nii.gz –vox2ras 2nd transform: mri_info –in path.pd.nii.gz –scanner2tkr 3rd transform: mri_inf –in orig.mgz –tkr2scanner I’ve tried some other sequence since I’m not sure what frame is the target output for the–vox2ras* transforms stored in path.pd.nii.gz . Those are the only transforms which contain the multiplication factors needed to get to millimeters from voxels. Rather than continuing to fumble around, some direction from you who know would be very much appreciated. Best - Don

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Fwd: Hippocampal subfields
by Ainara Gomez 22 Jan '19

22 Jan '19

External Email - Use Caution Hello, We have tried running hippocampal subfields module and we get an error with one of the subjects analyzed. Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c The error we get is the following (the log file has been attached): ransforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points numberOfLabels: 25 Rasterizing mesh...here: 25 Killed Started at Tue Jan 22 11:06:54 CET 2019 Ended at Tue Jan 22 11:25:14 CET 2019 #@#%# recon-all-run-time-hours 0.306 recon-all -s LR008 finished without error at Tue Jan 22 11:25:14 CET 2019 done Any help will be appreciated, Thank you very much, Leire -- -- Leire Zubiaurre-Elorza Assistant Professor Department of Methods and Experimental Psychology Faculty of Psychology and Education Tel.: +34 944 139 000-(ext.2299) Unibertsitateen Etorbidea, 24 48007 Bilbo-Bizkaia www.deusto.es -- -- Leire Zubiaurre-Elorza Assistant Professor Department of Methods and Experimental Psychology Faculty of Psychology and Education Tel.: +34 944 139 000-(ext.2299) Unibertsitateen Etorbidea, 24 48007 Bilbo-Bizkaia www.deusto.es

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Using PetSurfer to derive R1 values from early-phase dynamic PET
by Elijah Mak 22 Jan '19

22 Jan '19

External Email - Use Caution Hello Doug and PetSurfers, I would like to extract relative regional cerebral blood flow (R1) data from early time-interval of dynamic PET data (i.e. 11C-PiB) using the MRTM2 technique in PetSurfer. The time interval that I am interested in is between 0 and 6 minutes. Do you have any advice on how to go go about doing this? Thanks. Best Wishes, Elijah

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Tracula: Transform streamlines to T1 RAS coordinates
by Krieger, Donald N. 22 Jan '19

22 Jan '19

External Email - Use Caution I extract the streamlines for each tract from path.pd.trk to an ascii file and then wish to transform the coordinates to RAS T1 coordinates in millimeters. My results are not correct. Here is the extraction command I'm using. Is this correct? Perhaps I should be using orig.mgz as the outref volume? I do not understand -inref and --outref dmri_trk2trk -in path.pd.trk -inref path.pd.nii.gz -outref path.pd.nii.gz -outasc test.streamlines Given the above command, I am assuming that the output I'm getting is in the diffusion frame in voxel coordinates. I extract 4x4 transforms and apply them in sequence; I append 1.0 to each 3-vector before applying them of course. Here is the most compact approach I've tried 1st transform: mri_info -in path.pd.nii.gz -vox2ras-tkr 2nd transform: mri_info -in orig.mgz -tkr2scanner I've also tried this: 1st transform: mri_info -in path.pd.nii.gz -vox2ras 2nd transform: mri_info -in path.pd.nii.gz -scanner2tkr 3rd transform: mri_inf -in orig.mgz -tkr2scanner I've tried some other sequence since I'm not sure what frame is the target output for the-vox2ras* transforms stored in path.pd.nii.gz . Those are the only transforms which contain the multiplication factors needed to get to millimeters from voxels. Rather than continuing to fumble around, some direction from you who know would be very much appreciated. Best - Don

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Hippocampal subfields
by Leire Zubiaurre Elorza 22 Jan '19

22 Jan '19

1 0

回复： how to register feature maps to fsaverage6?
by 310913949 21 Jan '19

21 Jan '19

External Email - Use Caution Thanks for your reply! Actually, i first use "recon-all -s PT1_13 -i PT1_13.nii -all -qcache -target fsaverage6 " to process the subject, but i think i make some mistakes as i find there are about 110,000 vertex values in the"lh.thickness"file. and I also find that it generates a file named"recon-all.error",the context is as follows: Linux zhangjianing-Precision-Tower-7910 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26 18:10:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $ /media/root/533b526f-751c-4a6a-a3da-11856d602f84/usr/local/freesurfer/bin/recon-all PWD /media/root/533b526f-751c-4a6a-a3da-11856d602f84/usr/local/freesurfer/subjects/PT1_1302/surf CMD mris_preproc --s PT1_1302 --hemi lh --meas thickness --target fsaverage6 --out lh.thickness.fsaverage6.mgh" I am not sure whether i misused this command and how to correct that. Besides,i tried to use these two commands after recon-all, "mris_register -curv surf/lh.sphere $SUBJECTS_DIR/fsaverage6/lh.reg.template.tif surf/lh.sphere.reg.newtemplate" and"mris_preproc --s PT1_13--hemi lh --meas thickness --target $SUBJECTS_DIR/fsaverage6 --out lh.thickness.fsaverage6.mgh",but it didn't work. I also tried to use"mris_preproc --s PT1_1302 --hemi lh --meas thickness --target fsaverage6 --out lh.thickness.fsaverage6.mgh",but it didn't work too. So do you mean that i need to use"mris_surf2surf" after recon-all ?And am i wrong that i used above command lines to register subjects to fsaverage6? Thanks for any info! ------------------ 邓刊 Kan Deng E-mail：310913949(a)qq.com TEL：13728774014 ------------------ 原始邮件 ------------------ 发件人: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; 发送时间: 2019年1月22日(星期二) 上午10:37 收件人: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; 主题: Re: [Freesurfer] how to register feature maps to fsaverage6? are you feature maps already on individual subject surfaces? If so, you an use mri_surf2surf with fsaverage6 as the target cheers Bruce On Tue, 22 Jan 2019, 310913949 wrote: > > External Email - Use Caution > > Dear freesurfer experts?? > I want to know how to register feature maps to an average space (fsaverage6) so that I can get an identical > number of vertices(40962) for each hemisphere. Can you tell me what is the command line? > I am looking forward to your reply!Thanks. > > ------------------ > > ???? Kan Deng > > E-mail??310913949(a)qq.com > > TEL??13728774014 > > > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_watershed Error：Problem in the COG calculation
by Abby tang 21 Jan '19

21 Jan '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to recon-all subjects but for some of my subjects I get the following error when I run recon-all command: *************************WATERSHED************************** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. Linux abby-virtual-machine 4.15.0-43-generic #46-Ubuntu SMP Thu Dec 6 14:45:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 0078 exited with ERRORS at Sun Jan 20 20:16:12 CST 2019 I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. Thank you!

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consistent brain regions of Frontal_Sup_Medial_L(AAL) in freesurfer template
by charujing123 21 Jan '19

21 Jan '19

External Email - Use Caution Hi FS experts and users, I have an interested ROI Frontal_Sup_Medial_L in AAl. And I want to test the thickness or volume of this roi. I found some candidate roi in FS atlas, such as rostralanteriorcingulate, caudalanteriorcingulate, superiorfrontal. So which one is consistent with frontal_sup_medial in AAL. Thanks. rujing 2019-01-21 charujing123

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