Re: [Freesurfer] Fwd: segmentation error

2019-02-20 Thread mara alves 
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Hi,

Thanks for the quick reply. What do you mean about uploading the entire
subject? All the output files of the recon -all?

Best,
Mara

Bruce Fischl  escreveu no dia terça, 19/02/2019
à(s) 23:10:

> wow, that looks pretty bad. Can you send us the recon-all.log (or upload
> the entire subject and we will investigate)?
> On Tue, 19 Feb 2019, mara alves
> wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi there,
> >
> > I ran the recon -all command in two samples, one of young participants
> and another of older
> > subjects.
> >
> > The segmentation worked well for young participants, however it seems
> that for older participants
> > the white.pial segmentation it is being done incorrectly. I believe it
> is segmenting the gray matter
> > instead (please see the pics attached).
> >
> > Best,
> > Mara
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] Problem with freeview in linux subsystem for windows

2019-02-20 Thread falk.luesebr...@med.ovgu.de 
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Hi Brady,

do you run a X server on windows? I run Xming and included in the .bashrc 
"export DISPLAY=localhost:0.0".

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Williamson, Brady
Gesendet: Dienstag, 19. Februar 2019 21:51
An: Freesurfer support list 
Betreff: [Freesurfer] Problem with freeview in linux subsystem for windows


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Hi,

I am trying to run freeview in the linux subsystem (Ubuntu 18.04) for windows 
10 but keep getting the following error:

failed to get the current screen resources
QXcbConnection: XCB error: 170 (Unknown), sequence: 170, resource id: 90, major 
code: 146 (Unknown), minor code: 20
QXcbConnection: XCB error: 170 (Unknown), sequence: 170, resource id: 90, major 
code: 146 (Unknown), minor code: 20


Freeview opens but there is no image. Is there a fix for this issue?

Thanks,
Brady
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[Freesurfer] dtrecon

2019-02-20 Thread john Anderson 
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Hi FS experts,
I would like to inquire about the command "dtrecon" in Freesurfer.
Is this command able to process multishell diffusion data? if not would you 
recommend any method?

Thanks in advance
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[Freesurfer] mri_cc not giving thicker corpus callosum

2019-02-20 Thread DICE Lab 
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Dear FreeSurfer Developers,
I am trying to run the “mri_cc” command to obtain a segmentation of the
corpus callosum (CC) that is thicker then the usual 5mm (i.e. 5 voxel in my
image). I would like indeed to cover the "entire" CC volume and label it
with the canonical 5 values (let's say at least for the central CC, mid
anterior and mid posterior).

I tried
mri_cc -force -T 30 -aseg aseg.mgz -o aseg.auto_CC_30seg.mgz Control001

and it prints at screen
processing regardless of existence of cc in input volume
setting callosum thickness to 61 mm
will read input aseg from aseg.mgz
writing aseg with cc labels to aseg.auto_CC_30seg.mgz
reading aseg from /Users/Desktop/fsurfer/Control001/mri/aseg.mgz
reading norm from /Users/Desktop/fsurfer/Control001/mri/norm.mgz
97532 voxels in left wm, 30641 in right wm, xrange [126, 142]
MRIprincipleComponents: unsupported input type 1
No such file or directory
searching rotation angles z=[-7  7], y=[-7  7]
searching scale 1 Z rot 6.3  global minimum found at slice 132.0, rotations
(0.75, -0.50)
final transformation (x=132.0, yr=0.750, zr=-0.500):
 0.99988   0.00873   0.01309  -3.98366;
-0.00873   0.6  -0.00011   129.15181;
-0.01309   0.0   0.1   129.72784;
 0.0   0.0   0.0   1.0;
updating x range to be [127, 129] in xformed coordinates
best xformed slice 127
cc center is found at 127 0 0
MRIprincipleComponents: unsupported input type 1
No such file or directory
eigenvectors:
 0.0   0.0   0.0;
 0.0   0.0   0.0;
 0.0   0.0   0.0;
writing aseg with callosum to
/Users/Desktop/fsurfer/Control001/mri/aseg.auto_CC_30seg.mgz...
corpus callosum segmentation took 1.3 minutes


But when I open the file asset.auto_CC_30seg.mgz on the image brain.mgz I
still get a thickness of just 5 voxels. Could you please help me out in
understanding why?

I am wondering if this could be related to the warning
MRIprincipleComponents: unsupported input type 1
No such file or directory

But I do not understand to what it is referring to.
The input aseg.mgz looks fine to me and the command “recon_all” did not
give me any apparent issue.


I hope you can help me with this and I thank you in advance for your time.


Best regards,
Simona
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Re: [Freesurfer] Extracting anatomical locations for a set of RAS coordinates

2019-02-20 Thread Sparsh Jain 
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Hi Doug,

I tried what you suggested, but it did not work (see below for details of
what we tried). We have TkReg RAS coordinates (or vertex points) for our
electrode contacts; most contacts are *deep within the brain* (e.g.,
hippocampus and amygdala). We want to get a variable in Matlab that will
give us the anatomical labels as a function of the TkReg RAS coordinates
(or vertex points). How can we do this?

Thanks!

Sparsh

*What I tried:* I read the 'rh.aparc.2009a.annot' file in matlab using
read_annotation.m. That gave me 76 labels for right hemisphere, which I
believe correspond to the surface parcellations only. In freeview I loaded
the orig.mgz, aparc.a2009s+aseg.mgz, rh.pial and rh.inflated. I then
clicked on a cortical surface point to see if I can get the corresponding
vertex number or structure ID. On doing so, I found a value in the Vertex
row under rh.pial of freeview but this number wasn't found in the matlab
output (in the colortable.label or colortable.table). I think I am looking
in the wrong place to find the vertex # on freeview.

Also, I did not find a readable file for the segmentation data. I tried to
read the aparc.a2009s+aseg.mgz on Matlab but that didn't work.
Show quoted text

On Thu, 7 Feb 2019, 16:10 Greve, Douglas N.,Ph.D.  First, you'll have to find the closest vertex for each point in
> fsavarage. You can do this with by creating a label file then using
> mri_label2label with the --paint option.
>
> To find the label associated with each vertex, it is  probably easiest
> to use matlab using read_surf.m and read_annotation.m
>
> On 2/5/19 11:17 AM, Sparsh Jain wrote:
> >
> > External Email - Use Caution
> >
> > Good afternoon
> >
> > Is there is way to automatically extract the anatomical locations
> > corresponding to a set of RAS coordinates using Freesurfer's atlas? I
> > have a set of 200 points and I am trying to get their anatomical
> > labels automatically.
> >
> > Thank you
> > Sparsh
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] Fwd: segmentation error

2019-02-20 Thread Bruce Fischl 

Hi Mara

I mean.

cd $SUBJECTS_DIR
tar czvf subject.tgz $subject

then ftp the resulting subject.tgz file to our ftp site

cheers
Bruce

On Wed, 20 Feb 2019, mara alves wrote:



External Email - Use Caution

Hi,
Thanks for the quick reply. What do you mean about uploading the entire 
subject? All the output
files of the recon -all?

Best,
Mara

Bruce Fischl  escreveu no dia terça, 19/02/2019 
à(s) 23:10:
  wow, that looks pretty bad. Can you send us the recon-all.log (or upload
  the entire subject and we will investigate)?
  On Tue, 19 Feb 2019, mara alves
  wrote:

  >
  > External Email - Use Caution
  >
  > Hi there,
  >
  > I ran the recon -all command in two samples, one of young participants 
and another of
  older
  > subjects.
  >
  > The segmentation worked well for young participants, however it seems 
that for older
  participants
  > the white.pial segmentation it is being done incorrectly. I believe it 
is segmenting
  the gray matter
  > instead (please see the pics attached).
  >
  > Best,
  > Mara
  >
  >___
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  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Fwd: segmentation error

2019-02-20 Thread Bruce Fischl 
hmmm, I don't see anything glairing in the log. I guess upload the subject 
and we'll take a look

Bruce


On Wed, 20 Feb 2019, mara 
alves wrote:




External Email - Use Caution

Here is the recon-all.log for one for old subjects.Thanks,
Mara

mara alves  escreveu no dia quarta, 20/02/2019 à(s) 
09:57:
  Hi,
Thanks for the quick reply. What do you mean about uploading the entire 
subject? All the
output files of the recon -all?

Best,
Mara

Bruce Fischl  escreveu no dia terça, 19/02/2019 
à(s) 23:10:
  wow, that looks pretty bad. Can you send us the recon-all.log (or upload
  the entire subject and we will investigate)?
  On Tue, 19 Feb 2019, mara alves
  wrote:

  >
  > External Email - Use Caution
  >
  > Hi there,
  >
  > I ran the recon -all command in two samples, one of young participants 
and
  another of older
  > subjects.
  >
  > The segmentation worked well for young participants, however it seems 
that for
  older participants
  > the white.pial segmentation it is being done incorrectly. I believe it 
is
  segmenting the gray matter
  > instead (please see the pics attached).
  >
  > Best,
  > Mara
  >
  >___
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  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Problem with freeview in linux subsystem for

2019-02-20 Thread Williamson, Brady 
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Hi Falk,

Thank you for the reply. Yes, I am running Xming and have set this option in 
the .bashrc file. I still get the same error. I have tried to research this 
issue extensively but cannot seem to find the answer.

Thanks,
Brady
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Re: [Freesurfer] dtrecon

2019-02-20 Thread Greve, Douglas N.,Ph.D. 
It cannot. It just does simple tensor analysis. Not sure what else to use.

On 2/20/19 9:02 AM, john Anderson wrote:

External Email - Use Caution

Hi FS experts,
I would like to inquire about the command "dtrecon" in Freesurfer.
Is this command able to process multishell diffusion data? if not would you 
recommend any method?

Thanks in advance
John



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[Freesurfer] mri_convert

2019-02-20 Thread john Anderson 
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hi FS experts.
I would like to inquire about the command mri_ convert
I use this command to convert fMRI and PET 4D volumes from dicom format to 
nifti.

Are there any flags that can be used in mri_convert command line to enable it 
to extract a text file contain each series time in seconds?

thanks
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Re: [Freesurfer] Fwd: segmentation error

2019-02-20 Thread mara alves 
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Hi there,

Sorry for taking so long to respond but I am a newbie using Linux. I
uploaded the files using Martinos Center Filedrop under the subject --
Segmentation error - Mara - old suject file.

Thanks,
Mara

Bruce Fischl  escreveu no dia quarta,
20/02/2019 à(s) 15:13:

> hmmm, I don't see anything glairing in the log. I guess upload the subject
> and we'll take a look
> Bruce
>
>
> On Wed, 20 Feb 2019, mara
> alves wrote:
>
> >
> > External Email - Use Caution
> >
> > Here is the recon-all.log for one for old subjects.Thanks,
> > Mara
> >
> > mara alves  escreveu no dia quarta, 20/02/2019
> à(s) 09:57:
> >   Hi,
> > Thanks for the quick reply. What do you mean about uploading the entire
> subject? All the
> > output files of the recon -all?
> >
> > Best,
> > Mara
> >
> > Bruce Fischl  escreveu no dia terça,
> 19/02/2019 à(s) 23:10:
> >   wow, that looks pretty bad. Can you send us the recon-all.log (or
> upload
> >   the entire subject and we will investigate)?
> >   On Tue, 19 Feb 2019, mara alves
> >   wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Hi there,
> >   >
> >   > I ran the recon -all command in two samples, one of young
> participants and
> >   another of older
> >   > subjects.
> >   >
> >   > The segmentation worked well for young participants, however it
> seems that for
> >   older participants
> >   > the white.pial segmentation it is being done incorrectly. I
> believe it is
> >   segmenting the gray matter
> >   > instead (please see the pics attached).
> >   >
> >   > Best,
> >   > Mara
> >   >
> >   >___
> >   Freesurfer mailing list
> >   Freesurfer@nmr.mgh.harvard.edu
> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >___
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Re: [Freesurfer] registration and resampling in native space

2019-02-20 Thread Francesca Strappini 
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I'll try to find some visual way to show what I mean, but it's really
something mild and probably negligible.
Do you know if is it possible with mri_vol2vol to give to all the runs that
belong to the same subject the same system coordinates? So that each voxel
across runs will have the same coordinates. I noticed that the
transformation matrix is written in the header but it's not really applied
to the data. Thank you!


Best
Francesca


On Mon, Feb 18, 2019, 12:57 AM Bruce Fischl 
wrote:

> Hi Francesca
>
> can you send us an image that shows why you think it can be improved?
>
> cheers
> Bruce
> On
> Mon, 18 Feb 2019, Francesca Strappini wrote:
>
> >
> > External Email - Use Caution
> >
> > Thank you!Now the registration is better but still not perfect. Is there
> a way to improve it?
> >
> > Best
> >
> > Il giorno gio 14 feb 2019 alle ore 23:30 Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> ha
> > scritto:
> >   Is func_data.nii.gz an fMRI scan? If so, wouldn't be T2 weighted?
> If so,
> >   you should use --t2 instead of --t1 in bbregister
> >
> >   On 2/14/19 2:18 PM, Francesca Strappini wrote:
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Hi Doug,
> >   >
> >   > Could you advise me about how to correctly run mri_vol2vol?
> >   > The functional data did not get perfectly registered to the
> anatomy so
> >   > I'm afraid I'm not running it correctly.
> >   >
> >   > Thanks!
> >   >
> >   >
> >   > Il giorno mar 12 feb 2019 alle ore 17:21 Bruce Fischl
> >   > mailto:fis...@nmr.mgh.harvard.edu>>
> ha
> >   > scritto:
> >   >
> >   > Hi Francesca
> >   >
> >   > sorry, I defer to Doug on the details of mri_vol2vol.
> >   >
> >   > cheers
> >   > Bruce
> >   >
> >   > On Tue, 12 Feb 2019,
> >   > Francesca Strappini wrote:
> >   >
> >   > >
> >   > > External Email - Use Caution
> >   > >
> >   > > Thank you for the reply!
> >   > > I run:
> >   > > mri_vol2vol --reg register.dat --mov func_data.nii.gz
> --targ
> >   > > /usr/local/freesurfer/subjects/sub3/mri/T1.mgz --o
> >   > func_data_registered2T1.nii.gz --no-resample
> >   > >
> >   > > Then I checked the registration and it seems that the
> original
> >   > run is better aligned to the T1 than
> >   > > the registered one. Maybe am I not running mri_vol2vol
> correctly?
> >   > >
> >   > > Thanks!
> >   > > Best
> >   > >
> >   > >
> >   > > Il giorno mar 12 feb 2019 alle ore 02:19 Bruce Fischl
> >   >  fis...@nmr.mgh.harvard.edu>>
> >   > ha scritto:
> >   > >   Hi Francesca
> >   > >
> >   > >   check out the --no-resample option in mri_vol2vol.
> It just
> >   > changes the
> >   > >   header, so I think should do what you want.
> >   > >
> >   > >   cheers
> >   > >   Bruce
> >   > >
> >   > >
> >   > >   On Tue, 12 Feb 2019, Francesca Strappini wrote:
> >   > >
> >   > >   >
> >   > >   > External Email - Use Caution
> >   > >   >
> >   > >   > Dear Freesurfer's experts,
> >   > >   >
> >   > >   > I would like to register some functional data to
> the T1,
> >   > that were collected in
> >   > >   separate days.
> >   > >   > I used bbregister:
> >   > >   >
> >   > >   > bbregister --s sub3 --mov func_data.nii.gz - --reg
> >   > register.dat --init-coreg --t1
> >   > >   >
> >   > >   > Now, I would like to resample the data based on the
> >   > register.dat without upsampling
> >   > >   and keeping the
> >   > >   > same FoV (3x3x3 mm; 64 64 50). Is it doable?
> >   > >   >
> >   > >   > Thanks!
> >   > >   > Best
> >   > >   >
> >   > >   >
> >   > >   > --
> >   > >   > Francesca Strappini, Ph.D.
> >   > >   > Neurobiology Department
> >   > >   > Weizmann Institute of Science
> >   > >   > 234 Herzl Street, Rehovot 7610001 Israel
> >   > >   > Tel.: +972 58 444 2584
> >   > >   > E-mail: francesca.strapp...@weizmann.ac.il
> >   > 
> >   > >   >
> >   > >   >___
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> >   > 
> >   > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fr

Re: [Freesurfer] mri_convert

2019-02-20 Thread Adam Martersteck 
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mri_convert can do lots of things but I would actually try mri_probedicom
to get the DICOM timings. If you have AFNI installed you could also try
dicom_hinfo which has more examples in the AFNI wiki than mrI_probedicomi.
You could just loop over dicoms writing stdout to a text file.

On Wed, Feb 20, 2019 at 10:45 AM john Anderson 
wrote:

> External Email - Use Caution
>
> hi FS experts.
> I would like to inquire about the command mri_ convert
> I use this command to convert fMRI and PET 4D volumes from dicom format to
> nifti.
>
> Are there any flags that can be used in mri_convert command line to enable
> it to extract a text file contain each series time in seconds?
>
> thanks
> John
>
> ___
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[Freesurfer] Fw: clusters annotation file in surface - ERROR

2019-02-20 Thread Barletta, Valeria 
Thank you Doug,

As you suggested, I tried to use that command

(mris_seg2annot --seg lh.surf_combined-magn_CL_fwhm1.mgh --s MS072_R01_04 
--hemi lh --ctab MS072_R01_04.txt --o lh.cortical_les.annot)

but I got this error on tksurfer:

Successfully parsed tksurfer.tcl
reading white matter vertex locations...
% reading colortable from annotation file...
colortable with 7 entries read (originally MS072_R01_04.txt)
Found embedded color table in annotation.
131940 vertices did not have an annotation!
surfer: WARNING: no labels imported; annotation was empty


I attach my color table file...


Thanks for your help,

Vale



___


>Greve, Douglas N.,Ph.D. DGREVE at mgh.harvard.edu 
>
>Tue Feb 19 16:33:32 EST 2019

>You can create an annotation with mris_seg2annot (you basically have a
>surface-based segmentation). Run it with --help to get more info
>including examples. You will need to create your own color table

On 2/19/19 3:21 PM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I have a 3D volume mask of cortical lesions with 8 different clusters
> (8 cortical lesions).
>
> I projected this mask to the cortex and obtained a .mgh file with the
> command vol2surf:
>
> mri_vol2surf --src $path_to_lesion/$subj/combined-$lesion.nii.gz --out
> $path_to_output/$subj/surf/$hemi".surf_combined-"$lesion".mgh"
> --projfrac-avg -0.1 1 0.05 --hemi $hemi --regheader $subj
>
>
> Now I need to extract label files from this surface file, one
> label for each cluster, and then an annotation file summarizing all
> the label files.
>
> How can I do this?
>
> Thanks,
>
> Vale




From: Barletta, Valeria
Sent: Tuesday, February 19, 2019 3:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: clusters annotation file in surface


Dear Freesurfers,

I have a 3D volume mask of cortical lesions with 8 different clusters (8 
cortical lesions).

I projected this mask to the cortex and obtained a .mgh file with the command 
vol2surf:

mri_vol2surf --src $path_to_lesion/$subj/combined-$lesion.nii.gz --out 
$path_to_output/$subj/surf/$hemi".surf_combined-"$lesion".mgh" --projfrac-avg 
-0.1 1 0.05 --hemi $hemi --regheader $subj


Now I need to extract label files from this surface file, one label for each 
cluster, and then an annotation file summarizing all the label files.

How can I do this?

Thanks,

Vale





#$Id: FreeSurferColorLUT.txt,v 1.70.2.7 2012/08/27 17:20:08 nicks Exp $

#No. Label Name:R   G   B   A

0   Unknown 0   0   0   0
1   Lesion1 70  130 180 0
2   Lesion2 245 245 245 0
3   Lesion3 205 62  78  0
4   Lesion4 120 18  134 0
5   Lesion5 196 58  250 0
6   Lesion6 0   148 0   0
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Re: [Freesurfer] mris_preproc error: dimension mismatch

2019-02-20 Thread Peters, Douglas G 
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Hi Doug,

I'm still trying to troubleshoot my mris_preproc error: dimension mismatch.

I don't think qcache was run on the CBF images because they were last processed 
in SPM (working on old dataset made by someone else)...there aren't any smooth 
fwhm files.  Is it possible to run qcache on a nonnative freesurfer file? i.e. 
recon-all -s  -qcache -measure CBF.mgh?

Since I don't think this is an option I'm trying to run mri_surf2surf 
(--srcsubject subjid --srcsurfval subjid/surf/lh.CBF.fwhm10.mgh (ran in to type 
3 error when didn't specify the path) --trgsubject fsaverage --trgsurfval 
lh.thickness.fsaverage.mgh --hemi lh should I be using a different target 
file?

Hopefully this will solve my issue.

Also, is it possible that different FS versions create different vertices?  I 
am remaking my fsaverage with an older FS version to see if that may fix the 
issue.

Please let me know if my questions are unclear, and I will try to rephrase and 
add script input/output.

Thanks,
Doug P


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Greve, Douglas N.,Ph.D. 

Sent: Friday, February 15, 2019 8:26 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error: dimension mismatch

The subject surface probably changed since the last time you ran qcache and now 
has a different number of vertices. Try re-running qcache for those subjects.

On 2/15/19 2:58 AM, Peters, Douglas G wrote:

External Email - Use Caution

Hi Everyone,

I'm trying to prepare my Cerebral blood flow surface data for mri_glmfit group 
analysis (qdec doesn't allow you to choose your own subject surface files to 
analyze, so I figured mri_glmfit is my only option). Quick summary of what I 
did and where I get stuck:

##


I made a vol2surf conversion for some subject perfusion images hoping to 
evaluate CBF as if it were cortical thickness.  The original CBF volumes were 
registered and normalized in SPM and saved as CBF.nii all in same T1 space.  I 
made them into surface files using : mri_vol2surf --mov CBF.nii--regheader 
SubjectID --hemi rh --projfrac 0.5 --fwhm 10 --o CBF.mgh


I then tried to run:

mris_preproc --fsgd CBF.fsdg \

--cache-in CBF.fwhm10 \

--target fsaverage \

--hemi rh \

--out rh.CBF.10.mgh\


scans through all the subject .mghs

ninputs = # subjects

Checking inputs


"ERROR: dimension mismatch between" the first two surface files in my subject 
fsdg file


##


Please help. What should I do to get around this?


Thanks,

DP




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[Freesurfer] Special image protocol

2019-02-20 Thread mustafa amin 
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Dear member,

I am really new with this freesurfer, just need to ask 1 question. Is there a 
special image protocol before running the MRI and then upload it to freesurfer? 
Please share your thoughts. Thank you for your kind attention and cooperation.

Yours faithfully,

Mustafa M. Amin
Consultant Psychiatrist in Biological Psychiatry
Department of Psychiatry
Faculty of Medicine
Universitas Sumatera Utara


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