Hi Lee,
Thanks for your reply. I have repeated this step in
/Applications/freesurfer/subjects/HC001/mri using the following command:
mri_label2vol --seg left_thalamus.nii.gz --temp b0_brain.nii.gz --reg
registration2b0.dat --o left_thalamus_dwi_seed.nii.gz
And got this output:
Number of labels: 0
Annot File: (null)
Template Volume: b0_brain.nii.gz
Outut Volume: left_thalamus_dwi_seed.nii.gz
Registration File: registration2b0.dat
Fill Threshold: 0
Label Vox Vol: 1
ProjType: (null)
ProjTypeId: 0
ProjStart: 0
ProjStop: 0
ProjDelta: 0.1
Subject: (null)
Hemi: (null)
UseNewASeg2Vol: 1
DoLabelStatVol 0
LabelCodeOffset 0
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
$Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
Template RAS-to-Vox: --------
-0.400 0.000 0.000 64.000;
-0.000 -0.000 -0.400 48.000;
-0.000 0.400 -0.000 27.000;
0.000 0.000 0.000 1.000;
Template Voxel Volume: 15.625
nHits Thresh: 0
Loading registration from registration2b0.dat
RegMat: --------
0.996 0.088 -0.024 3.909;
0.025 -0.007 1.000 0.627;
0.088 -0.996 -0.009 -10.557;
0.000 0.000 0.000 1.000;
Label RAS-to-Vox: --------
-0.398 -0.035 0.010 62.436;
-0.035 0.398 0.004 52.223;
0.010 -0.003 0.400 27.251;
0.000 0.000 0.000 1.000;
ASeg2Vol: Building LUT
ASeg2Vol: Sorting
ASeg2Vol: Mapping
ASeg2Vol: Reverse Map
nmisses = 137063 (0 filled)
ASeg2Vol: done
I think everything is fine now?
Many thanks for your great help
André
________________________________________
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Lee Tirrell
[ltirr...@nmr.mgh.harvard.edu]
Gesendet: Donnerstag, 23. April 2015 20:15
An: Freesurfer support list
Betreff: Re: [Freesurfer] Using a2009s.annot as seed masks for tractography
Hi André,
Could you send the command that you ran to produce this ouput? Also (just to
check), do you have permissions to read the b0_brain.nii.gz file, and is it
here:
/Applications/freesurfer/subjects/HC001/b0_brain.nii.gz
Thanks,
Lee
On Thu, 23 Apr 2015, André Schmidt wrote:
> Dear Lee,
>
> Thanks a lot for your help. Unfortunately, now I've go the following error:
>
> Number of labels: 0
> Annot File: (null)
> Template Volume: b0_brain.nii.gz
> Outut Volume: left_thalamus_dwi_seed
> Registration File: registration2b0.dat
> Fill Threshold: 0
> Label Vox Vol: 1
> ProjType: (null)
> ProjTypeId: 0
> ProjStart: 0
> ProjStop: 0
> ProjDelta: 0.1
> Subject: (null)
> Hemi: (null)
> UseNewASeg2Vol: 1
> DoLabelStatVol 0
> LabelCodeOffset 0
> setenv SUBJECTS_DIR /Applications/freesurfer/subjects
> $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
> niiRead(): error opening file
> /Applications/freesurfer/subjects/HC001/b0_brain.nii.gz
> ERROR: reading b0_brain.nii.gz header
>
> I attach my b0_brain.nii.gz file. Do you know what's wrong?
>
> Thanks again
> André
> ________________________________________
> Von: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Lee
> Tirrell [ltirr...@nmr.mgh.harvard.edu]
> Gesendet: Freitag, 27. März 2015 19:07
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] Using a2009s.annot as seed masks for tractography
>
> On Thu, 26 Mar 2015, André Schmidt wrote:
> Hi Andre,
>
> Try using the --seg flag with vol2label, as in:
>
> mri_label2vol --seg left_putamen2.nii.gz --temp b0_brain.nii.gz --reg
> registration2b0.dat --o left_putamen_dwi_seed
>
> left_putamen2.nii.gz is a segmentation, where each voxel in the volume is
> assigned a number (in your case 1 for left putamen and 0 everywhere else).
> Freesurfer label files have a different format. Run mri_label2vol --help
> for more information. Hope this helps, and let us know if there are more
> problems.
>
> Best,
> Lee
>
>> Hi Anastasia,
>>
>> Sorry for not being clearer.
>>
>> According to your email, I have labelled all my regions of interest using
>> this command:
>>
>> "mri_binarize --match ID --i aparc.a2009s+aseg.mgz --o labelID.nii.gz"
>>
>> Let's take the left putamen as an example:
>>
>> "cmdline mri_binarize --match 12 --i aparc+aseg.mgz --o left_putamen2.nii.gz
>> sysname Darwin
>> hostname Andres-MacBook-Pro.local
>> machine x86_64
>> user andre
>>
>> input aparc+aseg.mgz
>> frame 0
>> nErode3d 0
>> nErode2d 0
>> output left_putamen2.nii.gz
>> Binarizing based on matching values
>> nMatch 1
>> 0 12
>> binval 1
>> binvalnot 0
>> Found 6228 values in range
>> Counting number of voxels
>> Found 6228 voxels in final mask
>> mri_binarize done"
>>
>> Please find attached the output file (left_putamen2.nii.gz).
>>
>> After this, I used the following command to create the register.dat file:
>>
>> "bbregister --s HC001 --mov HC001/mri/bo_brain.nii.gz --reg
>> HC001/mri/registration2b0.dat --dti --init-fsl"
>>
>> Please find attached the registration2b0.dat file.
>>
>> Then I wanted to convert the label file into diffusion space with
>> mri_label2vol with this command:
>>
>> "mri_label2vol --label left_putamen2.nii.gz --temp b0_brain.nii.gz --reg
>> registration2b0.dat --o left_putamen_dwi_seed
>> Number of labels: 1
>> left_putamen2.nii.gz
>> Annot File: (null)
>> Template Volume: b0_brain.nii.gz
>> Outut Volume: left_putamen_dwi_seed
>> Registration File: registration2b0.dat
>> Fill Threshold: 0
>> Label Vox Vol: 1
>> ProjType: (null)
>> ProjTypeId: 0
>> ProjStart: 0
>> ProjStop: 0
>> ProjDelta: 0.1
>> Subject: (null)
>> Hemi: (null)
>> UseNewASeg2Vol: 1
>> DoLabelStatVol 0
>> LabelCodeOffset 0
>> setenv SUBJECTS_DIR /Applications/freesurfer/subjects
>> $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
>> Template RAS-to-Vox: --------
>> -0.400 0.000 0.000 64.000;
>> -0.000 -0.000 -0.400 48.000;
>> -0.000 0.400 -0.000 27.000;
>> 0.000 0.000 0.000 1.000;
>> Template Voxel Volume: 15.625
>> nHits Thresh: 0
>> Loading registration from registration2b0.dat
>> RegMat: --------
>> 0.996 0.088 -0.024 3.909;
>> 0.025 -0.007 1.000 0.627;
>> 0.088 -0.996 -0.009 -10.557;
>> 0.000 0.000 0.000 1.000;
>> Label RAS-to-Vox: --------
>> -0.398 -0.035 0.010 62.436;
>> -0.035 0.398 0.004 52.223;
>> 0.010 -0.003 0.400 27.251;
>> 0.000 0.000 0.000 1.000;
>> nlabels = 1
>> Allocating Hit Volume (663552) voxels
>> Loading left_putamen2.nii.gz
>>
>> ??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????!
?!
> ????????????????????????????????????
>> mri_label2vol: could not scan # of lines from label file
>> ERROR reading left_putamen2.nii.gz"
>>
>>
>> Obviously something is wrong with the label file - do you see what I am
>> doing wrong?
>> Thank you
>> Andre
>> ________________________________________
>> Von: freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von
>> "Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
>> Gesendet: Dienstag, 17. März 2015 19:43
>> An: Freesurfer support list
>> Betreff: Re: [Freesurfer] Using a2009s.annot as seed masks for tractography
>>
>> Hi Andre - There is no way for us to guess what went wrong if we don't
>> know the output of the command that you're trying to run. For example,
>> "something went wrong" could mean that that the command failed without
>> creating any volume, that the volume was created but it doesn't look
>> right, etc.
>>
>> Please send us the command line that you type and all the text that the
>> command outputs on your terminal window.
>>
>> a.y
>>
>> On Tue, 17 Mar 2015, André Schmidt wrote:
>>
>>> Hi Anatasia,
>>>
>>> I was able to create a registration.dat with bbregister now ("bbregister
>>> --s HC001 --mov HC001/mri/bo_brain.nii.gz --reg
>>> HC001/mri/registration2b0.dat --dti --init-fsl"). However, I got an error
>>> message after using mri_label2vol - ERROR reading left_accumbens.nii.gz
>>>
>>> I think something went wrong with "mri_binarize --match ID --i
>>> aparc.a2009s+aseg.mgz --o labelID.nii.gz"
>>>
>>> For the left accumbens I used: "mri_binarize --match 12 --i aparc+aseg.mgz
>>> --o left_putamen.nii.gz"
>>>
>>> Sorry for this newbie question but I'm happy to get help
>>> Cheers
>>> Andre
>>> _______________________________
>>> Von: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von
>>> "Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
>>> Gesendet: Dienstag, 17. März 2015 16:59
>>> An: Freesurfer support list
>>> Betreff: Re: [Freesurfer] Using a2009s.annot as seed masks for tractography
>>>
>>> Hi Andre - What do you mean by diffusion file? The registration file that
>>> transforms between diffusion and anatomical space is output by bbregister
>>> (see part A of the tutorial that I mentioned below).
>>>
>>> a.y
>>>
>>> On Tue, 17 Mar 2015, André Schmidt wrote:
>>>
>>>> Hi Anastasia,
>>>>
>>>> I intend to use mri_label2vol to map the label file into the diffusion
>>>> space. Can you say me what for a diffusion file I can use for that and
>>>> where I can find it?
>>>>
>>>> Thanks again for your help
>>>> Andre
>>>> ________________________________________
>>>> Von: freesurfer-boun...@nmr.mgh.harvard.edu
>>>> [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von
>>>> "Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
>>>> Gesendet: Donnerstag, 26. Februar 2015 19:05
>>>> An: Freesurfer support list
>>>> Betreff: Re: [Freesurfer] Using a2009s.annot as seed masks for tractography
>>>>
>>>> Hi Andre - I'd go through the multimodal integration tutorial:
>>>>
>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview
>>>>
>>>> a.y
>>>>
>>>> On Thu, 26 Feb 2015, André Schmidt wrote:
>>>>
>>>>> Hi Anastasia,
>>>>>
>>>>> Thank you very much for your help. I have created such a label nii file,
>>>>> for example for ID 9, the left thalamus.
>>>>>
>>>>> Can you please help me how I can map that file into diffusion space using
>>>>> bbregister? I would like to use it then for probtrackx.
>>>>>
>>>>> Many thanks again.
>>>>> Andre
>>>>> ________________________________________
>>>>> Von: freesurfer-boun...@nmr.mgh.harvard.edu
>>>>> [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von
>>>>> "Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
>>>>> Gesendet: Donnerstag, 26. Februar 2015 16:09
>>>>> An: Freesurfer support list
>>>>> Betreff: Re: [Freesurfer] Using a2009s.annot as seed masks for
>>>>> tractography
>>>>>
>>>>> Hi Andre - You find the ID number of each of the regions you're interested
>>>>> in, from $FREESURFER_HOME/FreeSurferColorLUT.txt. Then you run:
>>>>> mri_binarize --match ID --i aparc.a2009s+aseg.mgz --o
>>>>> yourlabel.nii.gz
>>>>>
>>>>> Then you'll have to map that label into DWI space. We recommend bbregister
>>>>> for the cross-modal registration.
>>>>>
>>>>> a.y
>>>>>
>>>>> On Thu, 26 Feb 2015, André Schmidt wrote:
>>>>>
>>>>>> Dear freesurfer experts,
>>>>>> I intend to use the aparc.a2009s.annot file as seed regions for a
>>>>>> tractography analysis. I like to compute streamlines between every region
>>>>>> in the annot file. Can you please guide me how I can create masks for
>>>>>> every region in the annot file (or a text file with all seeds
>>>>>> including their paths)?
>>>>>>
>>>>>> Many thanks for your help.
>>>>>> Andre
>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
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