Re: [Freesurfer] Error in running make_average_subject

[Korom, Marta]

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Hello Bruce, Greve and Emanuel,

I have an identical problem. Have you found a solution to this issue? I'm
attaching my recon-all.log, as well, in case you need it.

Thank you!
Marta

On Fri, Dec 14, 2018 at 1:44 PM Emanuel Alvaredo 
wrote:

> External Email - Use Caution
>
> Thanks Greve. The output is attached  now.
>
>
> Emanuel
>
>
> On Fri, Dec 14, 2018 at 1:01 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>>  can you include the full terminal output?
>>
>> On 12/13/18 7:45 AM, Emanuel Alvaredo wrote:
>>
>> External Email - Use Caution
>> Hello Bruce, thanks for your anwer. Sure. The command is
>>
>> *make_average_subject --out avgsubjectPRUEBAESTASI! --subjects
>> Bartley_Recon Baez_Recon Bonilla_Recon*
>>
>> The output is in the attached file
>>
>> Thanks!
>>
>> Emanuel
>>
>>
>> On Wed, Dec 12, 2018 at 7:05 PM Bruce Fischl 
>> wrote:
>>
>>> Hi Emanuel,
>>>
>>> can you include the full command line and output?
>>>
>>> cheers
>>> Bruce
>>> On Wed, 12 Dec 2018,
>>> Emanuel Alvaredo wrote:
>>>
>>> >
>>> > External Email - Use Caution
>>> >
>>> > Thanks for your answer Douglas. I replaced the make_average_surface
>>> file with the new one but  I
>>> > have the same message error.
>>> > ASeg Vox2RAS: ---
>>> > -1.0   0.0   0.0   128.0;
>>> >  0.0   0.0   1.0  -128.0;
>>> >  0.0  -1.0   0.0   128.0;
>>> >  0.0   0.0   0.0   1.0;
>>> > mghRead(mri/norm.mgz, -1): could not open file
>>> > -
>>> >
>>> > Labeling Slice
>>> > relabeling unlikely voxels in interior of white matter
>>> > mri/norm.mgz: could not load norm volume from (null)
>>> >
>>> > Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2
>>> 17:16:02 UTC 2018 x86_64 x86_64
>>> > x86_64 GNU/Linux
>>> >
>>> > Thanks
>>> >
>>> > Emanuel
>>> >
>>> >
>>> > On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D. <
>>> dgr...@mgh.harvard.edu> wrote:
>>> >   Sorry, the disk that held that patch failed and we did not have
>>> a backup so not
>>> >   everything was restored. I just put this file there:
>>> >
>>> >
>>> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface
>>> >
>>> >   Copy it to $FREESURFER_HOME/bin. Let me know how it goes
>>> >
>>> >
>>> >   On 12/10/18 12:48 PM, Emanuel Alvaredo wrote:
>>> >
>>> >   External Email - Use Caution
>>> >
>>> >   Thanks Bruce. The following is the command.
>>> >
>>> >  make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects
>>> subject1
>>> > subject2 subject3
>>> >
>>> >
>>> > And I made a mistake in may last mail. I use the word path instead of
>>> patch
>>> >
>>> > I have found this page with a patch for de issue
>>> >
>>> >
>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
>>> >
>>> > But I dont know how to apply the patch. Can you give some information
>>> about this?
>>> >
>>> >
>>> > Emanuel
>>> >
>>> >
>>> > On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu> wrote:
>>> >   Hi Emanuel
>>> >
>>> >   you need to send us the full command you ran and output of it if
>>> you want
>>> >   us to be able to help you
>>> >
>>> >   cheers
>>> >   Bruce
>>> >   On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:
>>> >
>>> >   >
>>> >   > External Email - Use Caution
>>> >   >
>>> >   > Hello!, I am getting the following error using the
>>> >   command make_average_subject
>>> >   >
>>> >   > mri/norm.mgz: could not load norm volume from (null)
>>> >   >
>>> >   > I have found this page with a path for de issue
>>> >   >
>>> >   >
>>> >
>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
>>> >   >
>>> >   > But I dont know how to apply the path. Can you give some
>>> information about
>>> >   this?
>>> >   >
>>> >   > Thanks!
>>> >   >
>>> >   >
>>> >   >
>>> >   > Emanuel
>>> >   >
>>> >   >___
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>>> >
>>> >
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[Freesurfer] wm and vcsf nuisance regressors

[Nasiriavanaki, Zahra]

Dear Freesurfers


Hi

I am using white matter and CSF  external nuisance regressors in my 
mkanalysis-sess.

However, when I make these regressors, I use -mean in fcseed-config command, 
and so the .dat files only have one column (the mean values, I assume).

I looked up in the freesurfer archive and I saw that It is recommended to use  
-nuisreg wm.dat 5   and -nuisreg vcsf.dat 5.

My question is that what difference it makes to use mean of these regressors vs 
using only 5 of the columns.

I appreciate if you could please reply whenever you had time.


Thanks

Mona



Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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[Freesurfer] Help with finding which functional areas house certain electrodes

[Sparsh Jain]

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Good afternoon,

We want to find the functional areas where each electrode is located in
patients. At present, we are finding the electrode RAS coordinates manually
using CT-MRI co-registration. We are then manually searching for these
locations in Freeview using the aparc.a2009s+aseg  ATLAS (generated during
MRI reconstruction) on top of MRI volume. This is giving us the exact
anatomical/functional area where the electrode belongs. However, this is a
very tedious and time-consuming process and we need to do this for many
patients. We were wondering if there is
1. A way to automate this process by possibly entering all coordinates and
using the LUT and atlas files to get the areas easily for all points.

2. More importantly, could you tell us how to establish a method where we
can dump the anatomical region coordinates to a file, and then find the
nearest functional area to a particular electrode automatically? For
example, if a point lies in a white matter area, can we implement a process
to find which functional area (gray matter region, or say hippocampus for
example) lies CLOSEST to this electrode point in the white matter region.
Can we implement this automated process in an efficient manner for all the
points at once? We usually have anywhere between 140 -170 sets of
coordinates for each patient, and doing this by hand on freeview is not
practical.  Instead of finding where exactly all the points lie, we would
like to create a 'table' of all anatomical areas and then find out which
area of relevance lies closest to a particular point.

Thank you
Sparsh Jain
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Re: [Freesurfer] Issues parcellating with a custom atlas

[Michael Sughrue]

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Hi just following up on the question...
.does anyone have an idea about why the same two parcellations get dropped
when swapping the atlases out and making an aparc+aseg

On Mon, 14 Jan. 2019, 11:17 pm Michael Sughrue  Hello
>
> My interest is to create an aparc+aseg file with a combination of a
> cortical parcellation with a custom cortical atlas and the subcortical grey
> matter components from the standard asegbasically i want to mask and
> extract signal from multiple areas in a series of pipelines in python.  The
> commands below are called from python, but edited to make it easy to read.
>
>
> About 50% of the time the code below works fine, but the other 50% it
> drops two cortical parcellations.  Interestingly it is always the same two
> parcellations, both at the end of the left hemisphere list, that get
> dropped when making aparc+aseg.   My only guess is that something about the
> aparc and aseg combination is causing them to be dropped.
>
> I have read the annot files it makes and the parcellations are made in the
> mris_ca_label step and making the aparc+aseg.  I have viewed them in
> freeview and they are not there when viewed in the LUT for this atlas and I
> have tried omittng and excluding all forms of mri_binarize -replace
> commands (added to try to eliminate segmentations of the ventricle and
> white atter which i am trying to mask out of a resting state image), and
> this doesnt make a difference in the cases where it is failing.  I have
> tried using the cases where it worked to train a new gcs file without
> success.  I have also rune mri_aparc2aseg with and without the ribbon
> option, with all varieties of aseg files...etc etc.
>
> If there is something obviously wrong please let me know.  Alternately,
> what is the best way to get aparc+aseg.mgz to print a list of what areas
> made it in there..in that case i can likely create a way to make sure the
> lables it is using for an adjacency matrix atleast match the rows and
> columns accurately..i tried using segstats but this wasnt always an
> accurate list as it sometimes created a mask with areas not on any LUT's i
> have and thus i have been unable to view them in freeview or the segstats
> list and figure out what is going wrong
>
> the commands i invoke from python are below...thanks in advance
>
>
> recon-all -subjid sub1 -autorecon1 -openmp 6
> recon-all -subjid sub1 -autorecon2 -openmp 6
> 'recon-all -subjid sub1 -sphere -surfreg -jacobian_white -avgcurv -open mp6
>
> mris_ca_label -l $SUBJECTS_DIR/sub1/label/lh.cortex.label -aseg
> $SUBJECTS_DIR/sub1/mri/aseg.presurf.mgz sub1 lh lh.sphere.reg
> $SUBJECTS_DIR/sub1/parc/lh.hcp-mmp_6p0.gcs lh.aparc.annot
> mris_ca_label -l $SUBJECTS_DIR/sub1/label/rh.cortex.label -aseg
> $SUBJECTS_DIR/sub1/mri/aseg.presurf.mgz sub1 rh rh.sphere.reg
> $SUBJECTS_DIR/sub1/parc/rh.hcp-mmp_6p0.gcs rh.aparc.annot
> recon-all -subjid sub1 -pial -cortribbon -hyporelabel -openmp 6
> mri_binarize --i mri/aseg.presurf.hypos.mgz --o mri/aseg.mgz  --replace 2
> 0 --replace 4 0 --replace 5 0 --replace 7 0 --replace 14 0 --replace 15 0
> --replace 24 0 --replace 30 0 --replace 31 0 --replace 41 0 --replace 43 0
> --replace 44 0 --replace 46 0 --replace 62 0 --replace 63 0 --replace 77 0
> --replace 85 0 --replace 251 0 --replace 252 0 --replace 253 0 --replace
> 254 0  --replace 255 0')
> mri_aparc2aseg --s sub1
> mri_binarize --i mri/aparc+aseg.mgz --o mri/aparc+aseg.mgz --replace 41 0
>
>
>
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Re: [Freesurfer] mris_anatomical_stats input image?

[Bruce Fischl]

Hi Stephanie

specifying "pial" directs it to use the ?h.pial surfaces for e.g. surface 
area measurement. What information are you hoping to extract from the 
orig.mgz?


cheers
Bruce

On Thu, 17 Jan 2019, Winkelbeiner, Stephanie A wrote:



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Hi Freesurfers,

 

I’m using the below command to extract GM values:

mris_anatomical_stats -mgz \

    -cortex label/lh.cortex.label \

    -f stats/lh.250.aparc.pial.stats \

    -b -a 250.aparc \

    -c label/colortable.ctab \

    $subject lh pial

 

Specifying “pial” which image does the command actually use? The mri/orig.mgz?

 

Thanks for your help!

Stephanie

 

 


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[Freesurfer] mris_anatomical_stats input image?

[Winkelbeiner, Stephanie A]

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Hi Freesurfers,

I'm using the below command to extract GM values:
mris_anatomical_stats -mgz \
-cortex label/lh.cortex.label \
-f stats/lh.250.aparc.pial.stats \
-b -a 250.aparc \
-c label/colortable.ctab \
$subject lh pial

Specifying "pial" which image does the command actually use? The mri/orig.mgz?

Thanks for your help!
Stephanie




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attachments are intended only for the use of the individual or entity to whom 
or to which it is addressed, and may contain information that is privileged, 
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this communication is not the intended recipient, or the employee or agent 
responsible for delivering this communication to the intended recipient, you 
are hereby notified that any dissemination, distribution, copying or disclosure 
of this communication and any attachment is strictly prohibited. If you have 
received this transmission in error, please notify the sender immediately by 
telephone and electronic mail, and delete the original communication and any 
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Re: [Freesurfer] Exporting mean curvature indices

[Martin Juneja]

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Never mind, I just got it working by replacing "white.H" with "meancurv".

Thanks.

On Wed, Jan 16, 2019 at 5:32 PM Martin Juneja  wrote:

> Hi Freesurfer experts,
>
> I am interested in estimating mean curvature index for each of the 7
> networks (Yeo7 atlas) for my data of healthy controls. I am able to
> estimate this subjectwise, and the output stats file for each subject looks
> like following:
>
> # ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd
> MeanCurv GausCurv FoldInd CurvInd
> FreeSurfer_Defined_Medial_Wall   8952   5993   1906  0.916 1.370
>0.082 0.026   85 7.4
> 7Networks_1 23231  15309  34881  2.139 0.685
>0.125 0.028  26125.2
> 7Networks_2 20682  12735  35481  2.511 0.746
>0.101 0.022  16717.7
> 7Networks_3 14062   9362  24591  2.423 0.569
>0.107 0.021  12411.4
> 7Networks_4 12798   8490  25886  2.776 0.656
>0.109 0.023  11511.4
> 7Networks_5 10915   7302  26939  3.047 0.899
>0.122 0.030  13312.6
> 7Networks_6 15373  10259  28312  2.539 0.698
>0.123 0.027  16415.9
> 7Networks_7 32448  21779  70662  2.773 0.695
>0.124 0.028  37536.0
>
> I have 123 such files from a set of 123 subjects. I was just wondering how
> can I save mean curvature indices from all the subjects in one file (text
> or excel)? I defined my Subjects.txt file with subject IDs of each subject.
> I am not sure how to proceed from there to save curvature indices.
>
> I tried to run following command, but that does not work:
>
> aparcstats2table --subjectsfile Subjects.txt --hemi lh  --meas white.H -t
> MCI.txt
>
> I would really appreciate any help.
>
>
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Re: [Freesurfer] convert surface-based label to volumetric space...mri_label2vol?

[Greve, Douglas N.,Ph.D.]

You can extract it with
mri_binarize --i aparc+aseg.mgz --match 1027 --o 
ctx-lh-rostralmiddlefrontal.nii.gz
1027 comes from $FREESURFER_HOME/FreeSurferColorLUT.txt


On 1/17/19 11:31 AM, Stephanie Hare wrote:
>
> External Email - Use Caution
>
> Hi Doug,
>
> I converted the aparc+aseg.mgz file for the first 4 subjects using 
> mri_convert command as you suggested. Opening the files in an image 
> viewer shows the full brain parcellations for each subject (see 
> below). Is there a file (.mgz or other filetype) that specifically 
> parcellates the lh_rostralmiddlefrontal region? I want to generate a 
> mask of that region that can be used in 3D volumetric space for a 
> resting-state seed (left rostral-middle-frontal) to voxel connectivity 
> analysis. I'm worried this may be tricky given that this is a 
> 2D-surface-based atlas measurement applied at the single subject 
> level, and I was looking to generate and apply a single binary mask in 
> 3D space to all 100 schizophrenia patients' normalized functional 
> scans. Any suggestions? I appreciate your input.
>
> Cheers,
>
> Stephanie
>
> image.png
>
> On Tue, Jan 15, 2019 at 4:50 PM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> There should already be two volumes (aparc+aseg.mgz and
> aparc.a2009s+aseg.mgz) which you can simply convert to nifti with
> mri_convert file.mgz file.nii.gz
>
>
> On 1/15/19 2:14 PM, Stephanie Hare wrote:
> >
> > External Email - Use Caution
> >
> > Good afternoon,
> >
> > I'm new to Freesurfer; my background is resting-state fMRI using
> SPM.
> > Years back, left and right cortical thickness measures were
> calculated
> > for our sample of schizophrenia patients using the Desikan-Killiany
> > atlas and were input to an SPSS spreadsheet. In an exploratory
> > analysis of the data, I found that behavioral performance on a
> skills
> > assessment was correlated with thickness of lh_rostralmiddlefrontal
> > and lh_parstriangularis regions.
> >
> > I'd like to perform a follow-up resting-state fMRI analysis, using
> > these two surface-based parcellations ( lh_rostralmiddlefrontal and
> > lh_parstriangularis) as seed regions and use those behavioral
> > performance scores as a regressor.  Is there a simple way to
> convert
> > these two 2D-surface-based atlas measurements to masks in nifti
> format
> > in 3D-volumetric space? I was doing a quick google search and came
> > across the mri_label2vol command. Would this be helpful? Sorry for
> > my naiveté. I appreciate your time.
> >
> > Best,
> >
> > Stephanie Hare
> > Postdoctoral Fellow
> > Neuroimaging Research Program
> > Maryland Psychiatric Research Center
> >
> > ___
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> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>
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>
>
> -- 
> Stephanie Hare
> PhD Candidate
> Neuroscience Institute
> Georgia State University
>
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Re: [Freesurfer] Talairach Transform failure

[Greve, Douglas N.,Ph.D.]

The first thing to do is to check your input data to make sure that 
something is not really wrong. Eg, a large artifact or unusual anatomy.

On 1/17/19 5:35 AM, Daniel Ferreira wrote:
>
> External Email - Use Caution
>
> Thanks Greve. Yes, I mean that the moveable is completely black. How 
> should I continue from here? If the registration is so far off that it 
> is out
> of the field of view, what should I do next?
>
> Thanks
>
> Dani
>
> El mié., 16 ene. 2019 a las 22:54, Greve, Douglas N.,Ph.D. 
> (mailto:dgr...@mgh.harvard.edu>>) escribió:
>
> when you say it does not load, do you mean that the moveable is
> blank/black? The terminal output indicates that it is being
> loaded. It
> is probably the case that the registration is so far off that it
> is out
> of the field of view
>
> On 1/16/19 11:30 AM, Daniel Ferreira wrote:
> >
> > External Email - Use Caution
> >
> > Hi Greve,
> >
> > Thanks for your quick reply.
> >
> > I mean that tkregister2 loads the target volume (I think the
> original
> > T1 it is) but it does not load the moveable volume as stated in
> >
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview:
>
> > "You will see the subject's volume as the TARGET volume and your
> > Talairach volume as a fuzzy MOVEABLE volume ...".
> >
> > Below you will find the terminal output from tkregister2. Thanks in
> > advance.
> >
> > >>
> >
> > tkregister2 --mgz --s 0e63e2e7-d1e1-4e78-9106-150994a32c44 --fstal
> > tkregister_tcl /usr/local/freesurfer-6.0.0/tktools/tkregister2.tcl
> > INFO: no target volume specified, assuming FreeSurfer orig volume.
> > target  volume orig
> > movable volume (null)
> > reg file       (null)
> > LoadVol        1
> > ZeroCRAS       1
> > $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
> > Diagnostic Level -1
> >
> > %Tue Dec 11 11:32:27 2018>>>
> > /usr/local/freesurfer-6.0.0/mni/bin/minctracc -clobber -debug
> > /tmp/5039.1.all.q/mritotal_2474//src_8_dxyz.mnc
> >
> 
> /usr/local/freesurfer-6.0.0/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc
>
> > transforms/talairach.auto.xfm -transformation
> > /tmp/5039.1.all.q/mritotal_2474//src_8tmp2c.xfm -lsq9 -xcorr
> > -model_mask
> >
> 
> /usr/local/freesurfer-6.0.0/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc
>
> > -center -3.237066 24.478743 -30.435196 -step 4 4 4 -tol 0.004
> -simplex 2
> >
> > talairach.xfm -
> >  0.58327   0.88352  -0.65294  -43.57153;
> > -1.09786   0.44137  -0.38347  -72.94266;
> > -0.04069   0.75613   0.98680   212.60657;
> >  0.0   0.0   0.0   1.0;
> > INFO: loading target
> >
> /home/daniel/FreeSurfer/0e63e2e7-d1e1-4e78-9106-150994a32c44/mri/orig.mgz
> > Zeroing CRAS of target
> > new xfm -
> >  0.58327   0.88352  -0.65294  -25.73127;
> > -1.09786   0.44137  -0.38347  -65.12145;
> > -0.04069   0.75613   0.98680   228.56956;
> >  0.0   0.0   0.0   1.0;
> > -
> > INFO: changing target type to float
> > Ttarg: 
> > -1.0   0.0   0.0   128.0;
> >  0.0   0.0   1.0  -128.0;
> >  0.0  -1.0   0.0   128.0;
> >  0.0   0.0   0.0   1.0;
> > INFO: loading movable
> /usr/local/freesurfer-6.0.0/average/mni305.cor.mgz
> > INFO: changing move type to float
> > Tmov: 
> > -1.0   0.0   0.0   128.0;
> >  0.0   0.0   1.0  -128.0;
> >  0.0  -1.0   0.0   128.0;
> >  0.0   0.0   0.0   1.0;
> > mkheaderreg = 0, float2int = 0
> >  Input registration matrix 
> >  0.58327   0.88352  -0.65294  -25.73127;
> > -1.09786   0.44137  -0.38347  -65.12145;
> > -0.04069   0.75613   0.98680   228.56956;
> >  0.0   0.0   0.0   1.0;
> > Determinant 1.92442
> > subject = 0e63e2e7-d1e1-4e78-9106-150994a32c44
> > Zoom Factor = 2, SQR() = 4
> > FOV = 256
> > Opening window 0e63e2e7-d1e1-4e78-9106-150994a32c44
> > Opening 0e63e2e7-d1e1-4e78-9106-150994a32c44, xnum = 256, xdim = 512
> > Setting scale
> > tkregister2: interface:
> > /usr/local/freesurfer-6.0.0/tktools/tkregister2.tcl
> > tkregister.tcl: startup done
> > tkregister.tcl: default macro interface (to change:
> macro,mini,micro)
> > tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
> > % 
> >   Screen:  249 340 (28,28,28), inorm = 1, mov_frame = 0
> >   Anat:    (124  85 127)   (   4.0   -1.0   43.0)  32.    27.7
> >   Func:    (180 -142  42)   ( -52.4  -86.4  

Re: [Freesurfer] Talairach Transform failure

[Daniel Ferreira]

External Email - Use Caution

Thanks Greve. Yes, I mean that the moveable is completely black. How should
I continue from here? If the registration is so far off that it is out
of the field of view, what should I do next?

Thanks

Dani

El mié., 16 ene. 2019 a las 22:54, Greve, Douglas N.,Ph.D. (<
dgr...@mgh.harvard.edu>) escribió:

> when you say it does not load, do you mean that the moveable is
> blank/black? The terminal output indicates that it is being loaded. It
> is probably the case that the registration is so far off that it is out
> of the field of view
>
> On 1/16/19 11:30 AM, Daniel Ferreira wrote:
> >
> > External Email - Use Caution
> >
> > Hi Greve,
> >
> > Thanks for your quick reply.
> >
> > I mean that tkregister2 loads the target volume (I think the original
> > T1 it is) but it does not load the moveable volume as stated in
> > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview:
>
> > "You will see the subject's volume as the TARGET volume and your
> > Talairach volume as a fuzzy MOVEABLE volume ...".
> >
> > Below you will find the terminal output from tkregister2. Thanks in
> > advance.
> >
> > >>
> >
> > tkregister2 --mgz --s 0e63e2e7-d1e1-4e78-9106-150994a32c44 --fstal
> > tkregister_tcl /usr/local/freesurfer-6.0.0/tktools/tkregister2.tcl
> > INFO: no target volume specified, assuming FreeSurfer orig volume.
> > target  volume orig
> > movable volume (null)
> > reg file   (null)
> > LoadVol1
> > ZeroCRAS   1
> > $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
> > Diagnostic Level -1
> >
> > %Tue Dec 11 11:32:27 2018>>>
> > /usr/local/freesurfer-6.0.0/mni/bin/minctracc -clobber -debug
> > /tmp/5039.1.all.q/mritotal_2474//src_8_dxyz.mnc
> >
> /usr/local/freesurfer-6.0.0/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc
>
> > transforms/talairach.auto.xfm -transformation
> > /tmp/5039.1.all.q/mritotal_2474//src_8tmp2c.xfm -lsq9 -xcorr
> > -model_mask
> >
> /usr/local/freesurfer-6.0.0/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc
>
> > -center -3.237066 24.478743 -30.435196 -step 4 4 4 -tol 0.004 -simplex 2
> >
> > talairach.xfm -
> >  0.58327   0.88352  -0.65294  -43.57153;
> > -1.09786   0.44137  -0.38347  -72.94266;
> > -0.04069   0.75613   0.98680   212.60657;
> >  0.0   0.0   0.0   1.0;
> > INFO: loading target
> > /home/daniel/FreeSurfer/0e63e2e7-d1e1-4e78-9106-150994a32c44/mri/orig.mgz
> > Zeroing CRAS of target
> > new xfm -
> >  0.58327   0.88352  -0.65294  -25.73127;
> > -1.09786   0.44137  -0.38347  -65.12145;
> > -0.04069   0.75613   0.98680   228.56956;
> >  0.0   0.0   0.0   1.0;
> > -
> > INFO: changing target type to float
> > Ttarg: 
> > -1.0   0.0   0.0   128.0;
> >  0.0   0.0   1.0  -128.0;
> >  0.0  -1.0   0.0   128.0;
> >  0.0   0.0   0.0   1.0;
> > INFO: loading movable /usr/local/freesurfer-6.0.0/average/mni305.cor.mgz
> > INFO: changing move type to float
> > Tmov: 
> > -1.0   0.0   0.0   128.0;
> >  0.0   0.0   1.0  -128.0;
> >  0.0  -1.0   0.0   128.0;
> >  0.0   0.0   0.0   1.0;
> > mkheaderreg = 0, float2int = 0
> >  Input registration matrix 
> >  0.58327   0.88352  -0.65294  -25.73127;
> > -1.09786   0.44137  -0.38347  -65.12145;
> > -0.04069   0.75613   0.98680   228.56956;
> >  0.0   0.0   0.0   1.0;
> > Determinant 1.92442
> > subject = 0e63e2e7-d1e1-4e78-9106-150994a32c44
> > Zoom Factor = 2, SQR() = 4
> > FOV = 256
> > Opening window 0e63e2e7-d1e1-4e78-9106-150994a32c44
> > Opening 0e63e2e7-d1e1-4e78-9106-150994a32c44, xnum = 256, xdim = 512
> > Setting scale
> > tkregister2: interface:
> > /usr/local/freesurfer-6.0.0/tktools/tkregister2.tcl
> > tkregister.tcl: startup done
> > tkregister.tcl: default macro interface (to change: macro,mini,micro)
> > tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
> > % 
> >   Screen:  249 340 (28,28,28), inorm = 1, mov_frame = 0
> >   Anat:(124  85 127)   (   4.0   -1.0   43.0)  32.27.7
> >   Func:(180 -142  42)   ( -52.4  -86.4  270.1) OutOfBounds
> > --
> >
> >
> >
> >
> >
> > El mié., 16 ene. 2019 a las 15:35, Greve, Douglas N.,Ph.D.
> > (mailto:dgr...@mgh.harvard.edu>>) escribió:
> >
> > What do you mean that the tal volume does not load as a mov
> > volume? Can you send the terminal output from tkregister2?
> >
> > On 1/16/19 10:01 AM, Daniel Ferreira wrote:
> >>
> >> External Email - Use Caution
> >>
> >> Dear Bruce, Martin, and experts,
> >>
> >>
> >> I posted an issue a few days ago. I have been looking through the
> >> archives but can not figure out the