External Email - Use Caution
hi,FreeSurfer experts. I am trying to use segmentHA_T2.sh command to segment the T2 FLAIR Sequence MRI Data. Also I am now only having T2 Data. But there was a mistake in the first step. Sincerely ask for help.
(1)First I use recon-all command to generate the subject file from my nii file.But it stop in Correct Defect step. I have run three times after 48 hours. It also stop there. I dont't know why. Can you help me?
my command: recon-all -all -i nii-004/ADNI_004_3D_FLAIR.nii.gz -s Subj004 -itkthreads 4
The output of the terminal is as follows： CORRECTING DEFECT 45 (vertices=24, convex hull=53, v0=135114) After retessellation of defect 45 (v0=135114), euler #=96 (83072,238273,155297) : difference with theory (-19) = -115 CORRECTING DEFECT 46 (vertices=97, convex hull=30, v0=136402) After retessellation of defect 46 (v0=136402), euler #=97 (83078,238301,155320) : difference with theory (-18) = -115 CORRECTING DEFECT 47 (vertices=74, convex hull=24, v0=138982) After retessellation of defect 47 (v0=138982), euler #=98 (83088,238338,155348) : difference with theory (-17) = -115 CORRECTING DEFECT 48 (vertices=83, convex hull=55, v0=139717) After retessellation of defect 48 (v0=139717), euler #=99 (83098,238391,155392) : difference with theory (-16) = -115 CORRECTING DEFECT 49 (vertices=141431, convex hull=17606, v0=149662)
(2)Because of the above mistakes, I haven't tried the next step yet. segmentHA_T2.sh subject004 ADNI_004_3D_FLAIR.nii.gz T2 0
(3)Attached is the log(recon-all.log).
(4)My envientment as follows: Ubuntu 16.04 amd_x64 freesurfer-linux-centos6_x86_64-dev.tar.gz(21-Nov-2018) My data type: 3D-FLAIR (Pixel Spacing X=1.0 mm; Pixel Spacing Y=1.0 mm; Pulse Sequence=SE/IR; Slice Thickness=1.2000000476837158 mm; TE=441.0 ms; TI=1650.0 ms; TR=4800.0 ms; Weighting=T2;)
Thanks, Qimo
External Email - Use Caution
Dear Qimo, You do need a T1 volume to run the main recon-all; sorry if the wiki wasn’t clear enough. It is true that segmenta_T2.sh only uses the intensities of the FLAIR scan, but a recon-all processed T1 is still necessary. Cheers, /E
-- Juan Eugenio Iglesias
ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London, and Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of qimo601 qimo601@126.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, 26 November 2018 at 06:49 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] segmentHA_T2.sh: amygdala recon-all command stoped.
External Email - Use Caution
hi,FreeSurfer experts. I am trying to use segmentHA_T2.sh command to segment the T2 FLAIR Sequence MRI Data. Also I am now only having T2 Data. But there was a mistake in the first step. Sincerely ask for help.
(1)First I use recon-all command to generate the subject file from my nii file.But it stop in Correct Defect step. I have run three times after 48 hours. It also stop there. I dont't know why. Can you help me?
my command: recon-all -all -i nii-004/ADNI_004_3D_FLAIR.nii.gz -s Subj004 -itkthreads 4
The output of the terminal is as follows： CORRECTING DEFECT 45 (vertices=24, convex hull=53, v0=135114) After retessellation of defect 45 (v0=135114), euler #=96 (83072,238273,155297) : difference with theory (-19) = -115 CORRECTING DEFECT 46 (vertices=97, convex hull=30, v0=136402) After retessellation of defect 46 (v0=136402), euler #=97 (83078,238301,155320) : difference with theory (-18) = -115 CORRECTING DEFECT 47 (vertices=74, convex hull=24, v0=138982) After retessellation of defect 47 (v0=138982), euler #=98 (83088,238338,155348) : difference with theory (-17) = -115 CORRECTING DEFECT 48 (vertices=83, convex hull=55, v0=139717) After retessellation of defect 48 (v0=139717), euler #=99 (83098,238391,155392) : difference with theory (-16) = -115 CORRECTING DEFECT 49 (vertices=141431, convex hull=17606, v0=149662)
(2)Because of the above mistakes, I haven't tried the next step yet. segmentHA_T2.sh subject004 ADNI_004_3D_FLAIR.nii.gz T2 0
(3)Attached is the log(recon-all.log).
(4)My envientment as follows: Ubuntu 16.04 amd_x64 freesurfer-linux-centos6_x86_64-dev.tar.gz(21-Nov-2018) My data type: 3D-FLAIR (Pixel Spacing X=1.0 mm; Pixel Spacing Y=1.0 mm; Pulse Sequence=SE/IR; Slice Thickness=1.2000000476837158 mm; TE=441.0 ms; TI=1650.0 ms; TR=4800.0 ms; Weighting=T2;)
Thanks,
Qimo
External Email - Use Caution
Dear Juan Eugenio Iglesias:
Thanks for the response. I have a question about T1 and T2 data, whether they must be scanned by the same patient? Because I have no T1 sequence data. If i want to get the hippocampal subfields of T2 data, can I use T1 data of patient A to recon-all and T2 data of another patient B to segment ?
Thank you very much. Confused beginner. Qimo
At 2018-11-26 23:45:17, "Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk wrote:
External Email - Use Caution
Dear Qimo,
You do need a T1 volume to run the main recon-all; sorry if the wiki wasn’t clear enough. It is true that segmenta_T2.sh only uses the intensities of the FLAIR scan, but a recon-all processed T1 is still necessary.
Cheers,
/E
External Email - Use Caution
While I guess it’d technically be possible to use the SAMSEG tools to obtain an initial ASEG, and then modify the hippocampal tool slightly to accommodate this change, I think that I’ll say that no, at this moment it is not possible – but maybe we should look into this in the future. Sorry if this is not the answer you’d have liked to hear… /E
-- Juan Eugenio Iglesias
ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London, and Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of qimo601 qimo601@126.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 27 November 2018 at 00:29 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] segmentHA_T2.sh: amygdala recon-all command stoped.
External Email - Use Caution
Dear Juan Eugenio Iglesias: Thanks for the response. I have a question about T1 and T2 data, whether they must be scanned by the same patient? Because I have no T1 sequence data. If i want to get the hippocampal subfields of T2 data, can I use T1 data of patient A to recon-all and T2 data of another patient B to segment ?
Thank you very much. Confused beginner. Qimo
At 2018-11-26 23:45:17, "Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk wrote:
External Email - Use Caution Dear Qimo, You do need a T1 volume to run the main recon-all; sorry if the wiki wasn’t clear enough. It is true that segmenta_T2.sh only uses the intensities of the FLAIR scan, but a recon-all processed T1 is still necessary. Cheers, /E
-- Juan Eugenio Iglesias
ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London, and Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of qimo601 <qimo601@126.commailto:qimo601@126.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, 26 November 2018 at 06:49 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] segmentHA_T2.sh: amygdala recon-all command stoped.
External Email - Use Caution
hi,FreeSurfer experts. I am trying to use segmentHA_T2.sh command to segment the T2 FLAIR Sequence MRI Data. Also I am now only having T2 Data. But there was a mistake in the first step. Sincerely ask for help.
(1)First I use recon-all command to generate the subject file from my nii file.But it stop in Correct Defect step. I have run three times after 48 hours. It also stop there. I dont't know why. Can you help me?
my command: recon-all -all -i nii-004/ADNI_004_3D_FLAIR.nii.gz -s Subj004 -itkthreads 4
The output of the terminal is as follows： CORRECTING DEFECT 45 (vertices=24, convex hull=53, v0=135114) After retessellation of defect 45 (v0=135114), euler #=96 (83072,238273,155297) : difference with theory (-19) = -115 CORRECTING DEFECT 46 (vertices=97, convex hull=30, v0=136402) After retessellation of defect 46 (v0=136402), euler #=97 (83078,238301,155320) : difference with theory (-18) = -115 CORRECTING DEFECT 47 (vertices=74, convex hull=24, v0=138982) After retessellation of defect 47 (v0=138982), euler #=98 (83088,238338,155348) : difference with theory (-17) = -115 CORRECTING DEFECT 48 (vertices=83, convex hull=55, v0=139717) After retessellation of defect 48 (v0=139717), euler #=99 (83098,238391,155392) : difference with theory (-16) = -115 CORRECTING DEFECT 49 (vertices=141431, convex hull=17606, v0=149662)
(2)Because of the above mistakes, I haven't tried the next step yet. segmentHA_T2.sh subject004 ADNI_004_3D_FLAIR.nii.gz T2 0
(3)Attached is the log(recon-all.log).
(4)My envientment as follows: Ubuntu 16.04 amd_x64 freesurfer-linux-centos6_x86_64-dev.tar.gz(21-Nov-2018) My data type: 3D-FLAIR (Pixel Spacing X=1.0 mm; Pixel Spacing Y=1.0 mm; Pulse Sequence=SE/IR; Slice Thickness=1.2000000476837158 mm; TE=441.0 ms; TI=1650.0 ms; TR=4800.0 ms; Weighting=T2;)
Thanks,
Qimo
freesurfer@nmr.mgh.harvard.edu
-
Iglesias Gonzalez, Eugenio -
qimo601