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 55.0000 17.0000 23.0000 52.2444 9.6043 41.6544 1 47.0000 1.0000 39.0000 43.8696 -10.7903 51.4429 2 52.0000 -4.0000 28.0000 49.1826 -11.6594 40.1300 3 55.0000 17.0000 16.0000 52.5536 11.8998 35.2230 4 50.0000 -10.0000 23.0000 47.4912 -15.6659 33.7380 Writing label file /dev/shm/32089_labels 33 mri_label2label: Done
Thanks - Don
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Krieger, Donald N. Sent: Wednesday, August 22, 2018 8:35 PM To: 'freesurfer@nmr.mgh.harvard.edu' 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 55.0000 17.0000 23.0000 52.2444 9.6043 41.6544 1 47.0000 1.0000 39.0000 43.8696 -10.7903 51.4429 2 52.0000 -4.0000 28.0000 49.1826 -11.6594 40.1300 3 55.0000 17.0000 16.0000 52.5536 11.8998 35.2230 4 50.0000 -10.0000 23.0000 47.4912 -15.6659 33.7380 Writing label file /dev/shm/32089_labels 33 mri_label2label: Done
Thanks - Don
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Krieger, Donald N. *Sent:* Wednesday, August 22, 2018 8:35 PM *To:* 'freesurfer@nmr.mgh.harvard.edu' 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 55.0000 17.0000 23.0000 52.2444 9.6043 41.6544
1 47.0000 1.0000 39.0000 43.8696 -10.7903 51.4429
2 52.0000 -4.0000 28.0000 49.1826 -11.6594 40.1300
3 55.0000 17.0000 16.0000 52.5536 11.8998 35.2230
4 50.0000 -10.0000 23.0000 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@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Krieger, Donald N.