Re: [Freesurfer] mri_label2label dependencies
Hi Don, sorry for the delay. It is using the talairach.xfm files in both subjects to do the mapping. doug On 08/24/2018 11:40 AM, Krieger, Donald N. wrote: > > External Email - Use Caution > > Dear freesurfers, > > I didn’t see a response to this but I might have missed it. > > In any case it looks like it’s working ok. > > I found an error in what I was doing which was confusing things. > > Best – Don > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > *On Behalf Of *Krieger, Donald N. > *Sent:* Wednesday, August 22, 2018 8:35 PM > *To:* 'freesurfer@nmr.mgh.harvard.edu' > *Subject:* [Freesurfer] mri_label2label dependencies > > *External Email - Use Caution * > > Dear freesurfers, > > I am using mri_label2label with –regmethod volume . > > The only other switches I am using are minimal as you can see below. > > The thing is that none of the freesurfer stuff is in the srcsubject’s > directory. > > Why is there no error message? > > Where is it getting the stuff below the line: Src2TrgVolReg: > --- ? > > Actually, I just need to know what to put into those directories so > this function will work properly. > > I see from the documentation that I need mri/transforms/talairach.xfm > in both the src and trg subject directories. > > Is there anything else that needs to be there? > > mri_label2label --trgsubject 174 --srcsubject subNo1 --trglabel > /dev/shm/32089_labels --srclabel /dev/shm/32089_tmp0-2 --regmethod volume > > srclabel = /dev/shm/32089_tmp0-2 > > srcsubject = subNo1 > > trgsubject = 174 > > trglabel = /dev/shm/32089_labels > > regmethod = volume > > usehash = 1 > > Use ProjAbs = 0, 0 > > Use ProjFrac = 0, 0 > > DoPaint 0 > > SUBJECTS_DIR /usr/local/pkg/freesurfer//subjects > > FREESURFER_HOME /usr/local/pkg/freesurfer/ > > Loading source label. > > Found 33 points in source label. > > Starting volumetric mapping 33 points > > Src2TrgVolReg: - > > 0.963 -0.002 -0.044 0.330; > > 0.034 0.930 -0.328 -0.544; > > 0.044 0.285 0.919 13.268; > > 0.000 0.000 0.000 1.000; > > 0 55. 17. 23. 52.2444 9.6043 41.6544 > > 1 47. 1. 39. 43.8696 -10.7903 51.4429 > > 2 52. -4. 28. 49.1826 -11.6594 40.1300 > > 3 55. 17. 16. 52.5536 11.8998 35.2230 > > 4 50. -10. 23. 47.4912 -15.6659 33.7380 > > Writing label file /dev/shm/32089_labels 33 > > mri_label2label: Done > > Thanks - Don > > > > ___ > 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] mri_label2label dependencies
External Email - Use Caution Dear freesurfers, I didn't see a response to this but I might have missed it. In any case it looks like it's working ok. I found an error in what I was doing which was confusing things. Best - Don From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Krieger, Donald N. Sent: Wednesday, August 22, 2018 8:35 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: [Freesurfer] mri_label2label dependencies External Email - Use Caution Dear freesurfers, I am using mri_label2label with -regmethod volume . The only other switches I am using are minimal as you can see below. The thing is that none of the freesurfer stuff is in the srcsubject's directory. Why is there no error message? Where is it getting the stuff below the line: Src2TrgVolReg: --- ? Actually, I just need to know what to put into those directories so this function will work properly. I see from the documentation that I need mri/transforms/talairach.xfm in both the src and trg subject directories. Is there anything else that needs to be there? mri_label2label --trgsubject 174 --srcsubject subNo1 --trglabel /dev/shm/32089_labels --srclabel /dev/shm/32089_tmp0-2 --regmethod volume srclabel = /dev/shm/32089_tmp0-2 srcsubject = subNo1 trgsubject = 174 trglabel = /dev/shm/32089_labels regmethod = volume usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR/usr/local/pkg/freesurfer//subjects FREESURFER_HOME /usr/local/pkg/freesurfer/ Loading source label. Found 33 points in source label. Starting volumetric mapping 33 points Src2TrgVolReg: - 0.963 -0.002 -0.044 0.330; 0.034 0.930 -0.328 -0.544; 0.044 0.285 0.919 13.268; 0.000 0.000 0.000 1.000; 0 55. 17. 23.52.2444 9.6043 41.6544 1 47. 1. 39.43.8696 -10.7903 51.4429 2 52. -4. 28.49.1826 -11.6594 40.1300 3 55. 17. 16.52.5536 11.8998 35.2230 4 50. -10. 23.47.4912 -15.6659 33.7380 Writing label file /dev/shm/32089_labels 33 mri_label2label: Done Thanks - Don ___ 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] mri_label2label dependencies
External Email - Use Caution Dear freesurfers, I am using mri_label2label with -regmethod volume . The only other switches I am using are minimal as you can see below. The thing is that none of the freesurfer stuff is in the srcsubject's directory. Why is there no error message? Where is it getting the stuff below the line: Src2TrgVolReg: --- ? Actually, I just need to know what to put into those directories so this function will work properly. I see from the documentation that I need mri/transforms/talairach.xfm in both the src and trg subject directories. Is there anything else that needs to be there? mri_label2label --trgsubject 174 --srcsubject subNo1 --trglabel /dev/shm/32089_labels --srclabel /dev/shm/32089_tmp0-2 --regmethod volume srclabel = /dev/shm/32089_tmp0-2 srcsubject = subNo1 trgsubject = 174 trglabel = /dev/shm/32089_labels regmethod = volume usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR/usr/local/pkg/freesurfer//subjects FREESURFER_HOME /usr/local/pkg/freesurfer/ Loading source label. Found 33 points in source label. Starting volumetric mapping 33 points Src2TrgVolReg: - 0.963 -0.002 -0.044 0.330; 0.034 0.930 -0.328 -0.544; 0.044 0.285 0.919 13.268; 0.000 0.000 0.000 1.000; 0 55. 17. 23.52.2444 9.6043 41.6544 1 47. 1. 39.43.8696 -10.7903 51.4429 2 52. -4. 28.49.1826 -11.6594 40.1300 3 55. 17. 16.52.5536 11.8998 35.2230 4 50. -10. 23.47.4912 -15.6659 33.7380 Writing label file /dev/shm/32089_labels 33 mri_label2label: Done Thanks - Don ___ 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.
