[Freesurfer] Fwd: View several Annot files in Tksurfer

[Faeze Vedaei]

Hi Freesurfer Experts,

In order to view specific annot files by tksurfer in Freesurfer, I used
mris_label2annot command to create annot files based on Destrieux atlas.
Now, I can import annot file in tksurfer, but just one file at the time. My
aim is to view several annot files by their specific colors in tksurfer
simultaneously. May you help me how can I do this? In advance, I'd
appreciate your consideration.

Regards,
Faezeh Vedaei
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Re: [Freesurfer] Fwd: Creare Annot File in Freesurface

[dgw]

try specifying the full path to the label.

hth
d

On Wed, Feb 24, 2016 at 2:37 PM, Faeze Vedaei  wrote:
> Hil Freesurfer experts,
>
> I am trying to create annot file in freesurface using mris_label2annot
> command. In this process, I got an error : cannot find or read
> 'labelfile'sname.label'. I want to help me and explain what is the problem I
> have such this error for every label file I practice? Here is the command
> line I used :
>
> mris_label2annot --s 002_S_0295 --h lh --ctab
> 002_S_0295/LABELS/aparc.annot.a2009s.ctab --a myaparc --l lh.G_orbital.label
>
> ERROR: cannot find or read lh.G_orbital.label.
>
>
> I'd appreciate it if you clarify me about this process and how I can solve
> this.
>
> Regards,
> Faezeh Vedaei
>
>
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[Freesurfer] Fwd: Creare Annot File in Freesurface

[Faeze Vedaei]

Hil Freesurfer experts,

I am trying to create annot file in freesurface using mris_label2annot
command. In this process, I got an error : cannot find or read
'labelfile'sname.label'. I want to help me and explain what is the problem
I have such this error for every label file I practice? Here is the command
line I used :

mris_label2annot --s 002_S_0295 --h lh --ctab
002_S_0295/LABELS/aparc.annot.a2009s.ctab --a myaparc --l lh.G_orbital.label

ERROR: cannot find or read lh.G_orbital.label.


I'd appreciate it if you clarify me about this process and how I can solve
this.

Regards,
Faezeh Vedaei
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[Freesurfer] Patch for ribbon.mgz failure

[Philip Deming]

Hi Freesurfer team,


I'm having an issue running -autorecon2. The program exits with errors because 
it is unable to create the ribbon.mgz file. According to the version 5.3 
release notes, there is a patch available to fix this issue:


Creation of the aseg.stats table fails when only running -autorecon1 or 
-autorecon2 because ribbon.mgz is not present. This has been fixed. Ask for a 
patch.


How can I obtain the patch to fix the ribbon.mgz issue?


Thanks,

Phil
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Re: [Freesurfer] Reading values from overlays with PETcoreg

[Pradeep]

Hello Doug,

I was wondering if there is a flag in the command  to obtain the SUVRs for
the same ROIs with out partial volume correction so that it would be easier
to compare.

Thanks,
Pradeep

On Fri, Jan 29, 2016 at 1:30 PM, Pradeep  wrote:

> It worked! Thank you!
> mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
> gtmseg.mgz --reg output.lta --replace-file seg.replace251.list --rescale
> 251 --mgx 0.01 --o gtmpvcRcc.output
>
> On Fri, Jan 29, 2016 at 12:23 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> The problem is that --default-seg-merge merges the CC with WM, so you
>> can't use that option, which means that you'll have to specify the rest
>> of the default seg merge manually. You can do this with more --replace
>> args or you can create a file. If you've been able to run mri_gtmpvc
>> without the current replace, then it will create a replacement file in
>> the aux folder. Get that, remove the 251 entry, and change the 252-255
>> entries to point to 251
>>
>> On 01/29/2016 02:12 PM, Pradeep wrote:
>> > Unfortunately, that did not fix the problem.
>> >
>> > Here is what I did
>> > 1)gtmseg --s 128_S_0225_v06 --keep-cc # noerrors
>> > 2)gtmseg --s 128_S_0225_v06 --keep-cc --no-xcerseg  # no errors
>> >
>> > 3)mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
>> > gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251
>> > --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o
>> > gtmpvcrcc.output
>> > Loading input t12pet.nii.gz
>> >   done loading input 1 frames
>> > ERROR: item 251 appears as both source and target seg id in
>> > replacement list
>> >
>> > $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $
>> > setenv SUBJECTS_DIR /analysis/software_test/fs6pvc
>> > cd /analysis/software_test/fs6pvc/128_S_0225_v06/mri
>> > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
>> > gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251
>> > --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o
>> > gtmpvcrcc.output
>> > sysname  Linux
>> > hostname
>> > machine  x86_64
>> > user
>> > vgthresh   0.001000
>> > nReplace   22
>> > 0. 0. 0. 0. 0. 0.
>> > 9 avail.processors, using 9
>> > Creating output directory gtmpvcrcc.output
>> > Loading seg for gtm gtmseg.mgz
>> > Loading seg ctab gtmseg.ctab
>> > Reading gtmseg.lta
>> > Replacing 22
>> > ERROR: CheckSegTissueType() no entry for seg 192
>> > Failed tissue type check
>> >
>> > Thank you for looking into this,
>> > Pradeep
>> >
>> >
>> > On Fri, Jan 29, 2016 at 10:13 AM, Douglas N Greve
>> > > wrote:
>> >
>> > I think I see the problem. When you run gtmseg, you need to add
>> > --keep-cc. You can rerun it using the previous command line, but add
>> > --keep-cc and --no-xcerseg. The second option tells it not to redo
>> the
>> > extracerebral segmentation (which won't change with CC)
>> >
>> > On 01/29/2016 11:21 AM, Pradeep wrote:
>> > > Thank you for the response.
>> > >
>> > > Here is my full command log with error
>> > >
>> > >
>> > > $gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc
>> > >
>> > > $ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01
>> --seg
>> > > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o
>> > > gtmpvccc.output
>> > > Loading input t12pet.nii.gz
>> > >   done loading input 1 frames
>> > >
>> > > $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $
>> > > setenv SUBJECTS_DIR /analysis/software_test/fs6pvc
>> > > cd /analysis/software_test/fs6pvc/**/mri
>> > > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
>> > > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o
>> > > gtmpvccc.output
>> > > sysname  Linux
>> > > hostname server
>> > > machine  x86_64
>> > > user user
>> > > vgthresh   0.001000
>> > > nReplace   18
>> > > 0. 0. 0. 0. 0. 0.
>> > > 9 avail.processors, using 9
>> > > Creating output directory gtmpvccc.output
>> > > Loading seg for gtm gtmseg.mgz
>> > > Loading seg ctab gtmseg.ctab
>> > > Reading gtmseg.lta
>> > > Replacing 18
>> > > ERROR: CheckSegTissueType() no entry for seg 192
>> > > Failed tissue type check
>> > >
>> > >
>> > > Thanks,
>> > > Pradeep
>> > >
>> > >
>> > > On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve
>> > > 
>> > > > >> wrote:
>> > >
>> > >
>> > >
>> > > On 01/28/2016 06:50 PM, Pradeep wrote:
>> > > > Hello Doug,
>> > > >
>> > > > I have used the gtmseg with --keep-cc flag and the
>> > > 

Re: [Freesurfer] bbregister problems

[Pradeep]

Thank you Douglas!
mri_coreg did an awesome job and the registration look good.


On Mon, Feb 22, 2016 at 7:51 PM, Douglas Greve 
wrote:

> If you have spm, you can use --init-spm. Alternatively, you can use
> mri_coreg instead of bbr (bbr is not as effective on blurry data)
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
>
> mri_coreg --s $fs --mov  ${pet_ext}_LIA.nii --lta output.lta
>
> Also, why is the top of the head cut off? That makes it much more
> difficult to register.
>
> doug
>
>
>
>
> On 2/22/16 8:02 PM, Pradeep wrote:
>
> Hello All,
>
> I am trying to map pet scans to MRI  using bbregister and quite a few
> subjects were improperly registered.
>
> Here are my steps:
> bbregister --s $fs --mov  ${pet_ext}_LIA.nii --init-fsl --t1 --lta
> output.lta
> tkregister2 --mov summed_LIA.nii --reg output.dat --surf
>
>
> [ mri]$ more output.dat.mincost
> 0.860663 0.000513 0.000492 -11.863233
> The first value is quite close to 1 so its bad
>
> I have attached a screen shot of the image and the log file generated
> after bbregister.
> Please let me know if there are any parameters that I could tweak to make
> the registration better.
>
> Thank you for your help,
> -Pradeep
>
>
>
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Re: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST

[Afzal, Afsana]

Hi Doug,

Upon reviewing the repeated measures ANOVA tutorial on the Freesurfer website I 
was able to revise the fsgd file (below) to what I now think is more accurate.

I'm treating each observation of a condition (risk-reward pairing) and 
indicating that each of those observations belong to the same subject 
(Subject1, Subject2, etc).

GroupDescriptorFile 1
Class Subject1
Class Subject2
VariableshRisk-vs-lRisk hRisk-vs-mRisk
Input Subject1-lRsk_lRwd Subject1 -1  0
Input Subject1-lRsk_mRwd Subject1 -1  0
Input Subject1-lRsk_hRwd Subject1 -1  0
Input Subject1-mRsk_lRwd Subject1 0  -1
Input Subject1-mRsk_mRwd Subject1 0  -1
Input Subject1-mRsk_hRwd Subject1 0  -1
Input Subject1-hRsk_lRwd Subject1 1   1
Input Subject1-hRsk_mRwd Subject1 1   1
Input Subject1-hRsk_hRwd Subject1 1   1

Input Subject2-lRsk_lRwd Subject1 -1  0
Input Subject2-lRsk_mRwd Subject1 -1  0
Input Subject2-lRsk_hRwd Subject1 -1  0
Input Subject2-mRsk_lRwd Subject1 0  -1
Input Subject2-mRsk_mRwd Subject1 0  -1
Input Subject2-mRsk_hRwd Subject1 0  -1
Input Subject2-hRsk_lRwd Subject1 1   1
Input Subject2-hRsk_mRwd Subject1 1   1
Input Subject2-hRsk_hRwd Subject1 1   1


Please let me know if you think this design looks more correct given the 
observations per subject.

Thanks for your help,
Afsana

__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana 
[aaf...@mgh.harvard.edu]
Sent: Monday, February 22, 2016 2:34 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST

Hi,

Sorry about the lack of clarification.

Yes, it's a functional study. Each of the classes is a subject. I basically 
want to compute the main effect of risk at the group level (i.e. High Risk 
minus Low Risk) but there are multiple observations per risk level since there 
are three different reward levels within each risk level (low Reward, med 
Reward, high Reward).
I was thinking of setting up all the risk-reward conditions as active (=1s) in 
the fsgd file and then subtracting the conditions using the contrast matrices 
below to get the main effect of Risk.

Please let me know if that makes a bit more sense.

Thanks for your help,
Afsana

__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, February 22, 2016 12:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST

I'm having a hard time deciphering what you are doing. Is this a
functional study? What are the 5 classes? Why are there all 1s
regardless of risk or reward level?

On 02/19/2016 10:52 AM, Afzal, Afsana wrote:
> Hi,
>
> I'm analyzing a decision making task with a 3x3 condition matrix:
> pairings of low, medium, high levels of risk with low, medium, high
> levels of reward.
>
> I've set up the following FSGD file to do a repeated
> measures/within-subject ANOVA:
>
> GroupDescriptorFile 1
> Class hc001
> Class hc002
> Class hc003
> Class hc004
> Class hc005
> Variables lRsk_lRwd lRsk_mRwd lRsk_hRwd mRsk_lRwd
> mRsk_mRwd mRsk_hRwd hRsk_lRwd hRsk_mRwd hRsk_hRwd
> Input hc001 hc001 1 1 1 1 1 1
> 1 1 1
> Input hc002 hc002 1 1 1 1 1 1
> 1 1 1
> Input hc003 hc003 1 1 1 1 1 1
> 1 1 1
> Input hc004 hc004 1 1 1 1 1 1
> 1 1 1
> Input hc005 hc005 1 1 1 1 1 1
> 1 1 1
>
> I've also created the following contrast matrices:
>
> Con1: Does difference between highRisk andLowRisk differ from 0?
> 0 0 0 0 0 -1 -1 -1 0 0 0 1 1 1
>
> Con2: Does difference between highRisk andMedRisk differ from 0?
> 0 0 0 0 0 0 0 0 -1 -1 -1 1 1 1
>
> Is this an appropriate way of setting up the ANOVA?
>
> Thanks for your help,
>
> Afsana
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
>
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