Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

[Douglas N Greve]

I'm still not sure why you are trying to do this. If FSL did not unpack 
the volumes with the correct orientation, then you need to switch to 
mri_convert. If they are in the right orientation, then I don't 
understand what you are trying to do.
doug

On 08/16/2016 05:27 PM, Afzal, Afsana wrote:
> Hi Doug,
>
> After the coregistration failed for the majority of the subjects, I visually 
> inspected a handful of the subjects in freeview and it looks like the 
> anatomical and the functional are reversed but I could be wrong.
>
> The nifti files are unpacked from DICOMs using unpack_fsl.sh 
> (/cluster/nrg/tools/0.10.0/code/lib/shell/unpack_fsl.sh). I can point you to 
> a specific subject directory if that would be of any help.
>
> Might be worth mentioning that the subjects who failed coreg were not scanned 
> using siemens scanners but Phillips and GE scanners. Don't know if there's 
> some sort of discrepancy between the scanner coordinate frames that could 
> potentially lead to this issue.
>
> Thank you very much 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: Tuesday, August 16, 2016 3:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
>
> How do you know that the structural is left-right reversed? Or that the
> fMRI is? How did you create the nifti files?
>
>
> On 08/16/2016 01:41 PM, Afzal, Afsana wrote:
>> Hi,
>>
>> I'm having trouble co-registering a bunch of subjects whose T1 is
>> left-right reversed. While the orientation of the structural file in
>> the NIfTI header is LIA and the orientation of the functional volume
>> is LAS, visual inspection shows that the structural is left-right
>> reversed. I then followed the steps outlined in
>> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
>>  to rerun
>> the reconstruction and re-registered the subject but the registration
>> mincost value is still hovering around 0.9 even with the left-right
>> reversed structural.
>>
>> I've tried running registration with SPM and FSL; neither method is
>> able to register these subjects properly.
>>
>> With --init-fsl I get the following:
>> WARNING: initial G-W contrast is negative, but expecting positive.
>> If the mov data has a T1 contrast, re-run with --T1
>>
>> and with --init-spm I get:
>> WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
>>   ... continuing.
>>
>> At this point I'm out of ideas to try out. This issue is occurring for
>> over 170 subjects (data collected outside Martinos using non-siemens
>> scanners).
>>
>> Any help would be much appreciated!
>>
>> Thanks,
>>
>> 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
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

[Afzal, Afsana]

Hi Doug, 

After the coregistration failed for the majority of the subjects, I visually 
inspected a handful of the subjects in freeview and it looks like the 
anatomical and the functional are reversed but I could be wrong. 

The nifti files are unpacked from DICOMs using unpack_fsl.sh 
(/cluster/nrg/tools/0.10.0/code/lib/shell/unpack_fsl.sh). I can point you to a 
specific subject directory if that would be of any help. 

Might be worth mentioning that the subjects who failed coreg were not scanned 
using siemens scanners but Phillips and GE scanners. Don't know if there's some 
sort of discrepancy between the scanner coordinate frames that could 
potentially lead to this issue.

Thank you very much 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: Tuesday, August 16, 2016 3:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

How do you know that the structural is left-right reversed? Or that the
fMRI is? How did you create the nifti files?


On 08/16/2016 01:41 PM, Afzal, Afsana wrote:
> Hi,
>
> I'm having trouble co-registering a bunch of subjects whose T1 is
> left-right reversed. While the orientation of the structural file in
> the NIfTI header is LIA and the orientation of the functional volume
> is LAS, visual inspection shows that the structural is left-right
> reversed. I then followed the steps outlined in
> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
>  to rerun
> the reconstruction and re-registered the subject but the registration
> mincost value is still hovering around 0.9 even with the left-right
> reversed structural.
>
> I've tried running registration with SPM and FSL; neither method is
> able to register these subjects properly.
>
> With --init-fsl I get the following:
> WARNING: initial G-W contrast is negative, but expecting positive.
> If the mov data has a T1 contrast, re-run with --T1
>
> and with --init-spm I get:
> WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
>  ... continuing.
>
> At this point I'm out of ideas to try out. This issue is occurring for
> over 170 subjects (data collected outside Martinos using non-siemens
> scanners).
>
> Any help would be much appreciated!
>
> Thanks,
>
> 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
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] Mixed anisotropic data

[Mahmoudi, Fariborz]

Dear Friends,

I have used a mixed set of images from 1.5T and 3.0T scanners with anisotropic 
voxel size in my study. I used Freesurfer tools for converting them to 
isotropic voxel size before segmentation and reconvert to initial state after 
segmentation. It is appreciated if someone let me know using such a mixed 
anisotropic data causes any side effect in the volume measurement or not. I 
will be also thankful if you could introduce a reference that discusses the 
effect.

Best Regards,
Fari



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Re: [Freesurfer] malloc_error_break/ can't allocate region

[miracle ozzoude]

FS 5.1.0. I tried it with 5000 reps for ROI analysis and it worked.

On Tue, Aug 16, 2016 at 3:46 PM, Douglas N Greve 
wrote:

> What version of FS (and mri_mcsim) are you using? Does it die if you run
> with just a few reps (eg, 100)?
>
> On 08/16/2016 01:21 PM, miracle ozzoude wrote:
> > Hello FreeSurfer team,
> > While running monte carlo correction with 1 reps (mri_mcsim) for
> > the whole hemisphere, I received this error at 975 reps for the left
> > hemisphere
> >
> > " 975 3197.9 0 mri_mcsim(25495) malloc: ***mmap(size=16777216) failed
> > (error code=12)
> > *** error: can't allocate region
> > *** set a breakpoint in malloc_error_break to debug
> > Bus error"
> > What does this mean and how can I resolve it? Below was my mri_mcsim
> > command line " mri_mcsim --o
> > wholebrainanalysis/average/mult-comp-cor/fsaverage/lh/cortex --base
> > mc-z --surface fsaverage lh --nreps 1"
> >
> > Thank you
> > Paul
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
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Re: [Freesurfer] Subject: Re: Zero cortical thickness

[Douglas N Greve]

which ROIs are coming up zero? Have you looked at the area maps for that 
subject for that ROI?

On 08/16/2016 01:16 PM, A Nunes wrote:
> I mean the area of an ROI
>
> On Tue, Aug 16, 2016 at 6:59 AM, Douglas N Greve
>  wrote:
>> please include previous correspondence. Do you mean the area of a vertex
>> or the area of an ROI?
>>
>> On 08/15/2016 06:06 PM, A Nunes wrote:
>>> Hi Douglas,
>>>
>>> I meant a surface area extracted from a surface based atlas.
>>>
>>> Thanks
>>> Adonay
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
> Hi
>
> I looked at the distribution areas with almost zero thickness and when
> I saw they were on one hemisphere, I checked my bash script and found
> out that for the left cortex it was calling the right hemisphere
> areas.
> However, I still have a few subjects which have zero thickness in some
> areas of my parcelled atlas. This zero thickness is it caused by a
> segmentation or a sphere reconstruction error/imperfection (in which
> case the value should be NaN), or is it capturing a brain structural
> characteristic worth to account for?
>
> Thanks
> Adonay
> Date: Mon, 15 Aug 2016 16:27:24 -0400
> From: Douglas Greve 
> Subject: Re: [Freesurfer] Zero cortical thickness
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <8c1593aa-77fc-333e-e7d7-1901f9a39...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> what do you mean by "area"? do you mean one of the cortical ROIs or do
> you mean a general location?
>
>
> On 8/15/16 4:13 PM, A Nunes wrote:
>> Hi,
>>
>> I have read in the mailing list about zero cortical thickness, but I
>> still have some doubts.
>>
>> I am calculating the average cortical thickness of some areas, and
>> there are a few that almost all the subjects' thickness is zero,
>> others only some subjects score zero. For the ones that almost all
>> subjects is zero, I would guess is not considered cortical, however,
>> all my areas are cortical.
>>
>> - If I compute a ttest against two groups, should I set the zeros as
>> NaNs? or are the zero thickness meaningful (a genuine measure or a
>> segmentation artifact)?
>>
>> -Should I use the -l ?h.cortex.label to avoid having zero thickness in
>> some areas? If so, at which point? the commands used are:
>>
>> mri_surf2surf --srcsubject fsaverage --trgsubject subjid --hemi ?h
>> --sval-annot fsaverage/label/?h.areas.annot --tval
>> $SUBJECTS_DIR/subjid/label/?h.areas.annot
>>
>> mris_anatomical_stats -a
>> $SUBJECTS_DIR/subjid/label/?h.areas.annot$SUBJECTS_DIR/subjid/label/?h.areas.annot
>>-f $SUBJECTS_DIR/subjid/stats/?h.areas.stats -b  subjid ?h
>>
>>
>> Thanks
>> Adonay
>> ___
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>>
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>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] malloc_error_break/ can't allocate region

[Douglas N Greve]

What version of FS (and mri_mcsim) are you using? Does it die if you run 
with just a few reps (eg, 100)?

On 08/16/2016 01:21 PM, miracle ozzoude wrote:
> Hello FreeSurfer team,
> While running monte carlo correction with 1 reps (mri_mcsim) for 
> the whole hemisphere, I received this error at 975 reps for the left 
> hemisphere
>
> " 975 3197.9 0 mri_mcsim(25495) malloc: ***mmap(size=16777216) failed 
> (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> Bus error"
> What does this mean and how can I resolve it? Below was my mri_mcsim 
> command line " mri_mcsim --o 
> wholebrainanalysis/average/mult-comp-cor/fsaverage/lh/cortex --base 
> mc-z --surface fsaverage lh --nreps 1"
>
> Thank you
> Paul
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

[Douglas N Greve]

How do you know that the structural is left-right reversed? Or that the 
fMRI is? How did you create the nifti files?


On 08/16/2016 01:41 PM, Afzal, Afsana wrote:
> Hi,
>
> I'm having trouble co-registering a bunch of subjects whose T1 is 
> left-right reversed. While the orientation of the structural file in 
> the NIfTI header is LIA and the orientation of the functional volume 
> is LAS, visual inspection shows that the structural is left-right 
> reversed. I then followed the steps outlined in 
> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal 
>  to rerun 
> the reconstruction and re-registered the subject but the registration 
> mincost value is still hovering around 0.9 even with the left-right 
> reversed structural.
>
> I've tried running registration with SPM and FSL; neither method is 
> able to register these subjects properly.
>
> With --init-fsl I get the following:
> WARNING: initial G-W contrast is negative, but expecting positive.
> If the mov data has a T1 contrast, re-run with --T1
>
> and with --init-spm I get:
> WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
>  ... continuing.
>
> At this point I'm out of ideas to try out. This issue is occurring for 
> over 170 subjects (data collected outside Martinos using non-siemens 
> scanners).
>
> Any help would be much appreciated!
>
> Thanks,
>
> 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
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] which CUDA version driver to use

[R Edgar]

On 15 August 2016 at 19:21, Karamfil Bahchevanov  wrote:

> I'd like to experiment with faster proceesing, in fact I'd like to try CUDA.
> However there are several possible drivers for my quadro K2000. I'm not sure
> which one to choose. Should I install the latest 7.5. version, or use the
> older version 6, or even older? I'm not sure if the latest will run with
> freesurfer smoothly.
> Here is my system: Xeon e5-1620, QUADRO K2000
> I'm running Freesurfer v5.3 on CentOS 6.8, kernel 2.6.32-642.1.1.el6.x86_64.

I've had success getting Freesurfer to compile with the CUDA 7.5
toolkit. You just have to make sure that the configure script is
really picking up your CUDA installation.

Regards,

Richard
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[Freesurfer] Bad Coregistration - Left-Right Reversed

[Afzal, Afsana]

Hi,

I'm having trouble co-registering a bunch of subjects whose T1 is left-right 
reversed. While the orientation of the structural file in the NIfTI header is 
LIA and the orientation of the functional volume is LAS, visual inspection 
shows that the structural is left-right reversed. I then followed the steps 
outlined in https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal to 
rerun the reconstruction and re-registered the subject but the registration 
mincost value is still hovering around 0.9 even with the left-right reversed 
structural.

I've tried running registration with SPM and FSL; neither method is able to 
register these subjects properly.

With --init-fsl I get the following:
WARNING: initial G-W contrast is negative, but expecting positive.
If the mov data has a T1 contrast, re-run with --T1

and with --init-spm I get:
WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
 ... continuing.

At this point I'm out of ideas to try out. This issue is occurring for over 170 
subjects (data collected outside Martinos using non-siemens scanners).

Any help would be much appreciated!

Thanks,

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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Re: [Freesurfer] Subject: Re: Zero cortical thickness

[A Nunes]

I mean the area of an ROI

On Tue, Aug 16, 2016 at 6:59 AM, Douglas N Greve
 wrote:
> please include previous correspondence. Do you mean the area of a vertex
> or the area of an ROI?
>
> On 08/15/2016 06:06 PM, A Nunes wrote:
>> Hi Douglas,
>>
>> I meant a surface area extracted from a surface based atlas.
>>
>> Thanks
>> Adonay
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>>
>>
Hi

I looked at the distribution areas with almost zero thickness and when
I saw they were on one hemisphere, I checked my bash script and found
out that for the left cortex it was calling the right hemisphere
areas.
However, I still have a few subjects which have zero thickness in some
areas of my parcelled atlas. This zero thickness is it caused by a
segmentation or a sphere reconstruction error/imperfection (in which
case the value should be NaN), or is it capturing a brain structural
characteristic worth to account for?

Thanks
Adonay


Date: Mon, 15 Aug 2016 16:27:24 -0400
From: Douglas Greve 
Subject: Re: [Freesurfer] Zero cortical thickness
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <8c1593aa-77fc-333e-e7d7-1901f9a39...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

what do you mean by "area"? do you mean one of the cortical ROIs or do
you mean a general location?


On 8/15/16 4:13 PM, A Nunes wrote:
> Hi,
>
> I have read in the mailing list about zero cortical thickness, but I
> still have some doubts.
>
> I am calculating the average cortical thickness of some areas, and
> there are a few that almost all the subjects' thickness is zero,
> others only some subjects score zero. For the ones that almost all
> subjects is zero, I would guess is not considered cortical, however,
> all my areas are cortical.
>
> - If I compute a ttest against two groups, should I set the zeros as
> NaNs? or are the zero thickness meaningful (a genuine measure or a
> segmentation artifact)?
>
> -Should I use the -l ?h.cortex.label to avoid having zero thickness in
> some areas? If so, at which point? the commands used are:
>
> mri_surf2surf --srcsubject fsaverage --trgsubject subjid --hemi ?h
> --sval-annot fsaverage/label/?h.areas.annot --tval
> $SUBJECTS_DIR/subjid/label/?h.areas.annot
>
> mris_anatomical_stats -a
> $SUBJECTS_DIR/subjid/label/?h.areas.annot$SUBJECTS_DIR/subjid/label/?h.areas.annot
>   -f $SUBJECTS_DIR/subjid/stats/?h.areas.stats -b  subjid ?h
>
>
> Thanks
> Adonay
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>
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Re: [Freesurfer] Subject: Re: Zero cortical thickness

[Douglas N Greve]

please include previous correspondence. Do you mean the area of a vertex 
or the area of an ROI?

On 08/15/2016 06:06 PM, A Nunes wrote:
> Hi Douglas,
>
> I meant a surface area extracted from a surface based atlas.
>
> Thanks
> Adonay
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>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] 'Invalid' license file

[zkaufman]

Hello Lee,

Opensuse platforms versions greater than 12.1 are not compatible with the
FreeSurfer licensing scheme, but their are workarounds. I will contact you
offline so we can figure out the best solution for your setup.

-Zeke



> Hi,
> Our IT department have recently upgraded our cluster OS and now Freesurfer
> complains that its license is invalid. I have tried rebuilding, and
> acquiring a new license, but these do not fix the problem. The license
> file I am using works in my Ubuntu 12.04 computer - it has been copied
> across as a file, not via a text editor - and used to work on an older
> version of the same OS.
>
> Do you know of any solution to this issue?
>
> I've tried everything I have seen on the mailing list, including naming it
> .license and license.txt, checking for whitespace, etc.
> Our OS is now SUSE Linux Enterprise Server 12 SP1 (x86_64).
>
> Many thanks,
> Lee
>
>
>
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[Freesurfer] pial_lgi table

[Chatzi, Vasiliki]

Dear developers,


I was wondering if you could let me know how can I extract a table for the 
measure pial_lgi.


Best wishes,

Vasiliki



Vasiliki Chatzi, BA(Hons) MSc
PhD student | Department of Psychosis studies
Institute of Psychiatry, Psychology and Neuroscience | King's College London
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Re: [Freesurfer] Error with long_mris_slopes: Surface files do not exist

[Martin Reuter]

Hi Nick,

it looks like the base finished without error. But if your *.long.basid/surf/ 
are missing the lh.thickness , then something went wrong when processing the 
-long runs. I would recommend to run a single subject step by step to see what 
goes wrong (could be IO problems or disk space etc). 

Best, Martin



> On Aug 15, 2016, at 11:06 PM, Corriveau-Lecavalier Nick 
>  wrote:
> 
> Hello FreeSurfer developers,
> 
> 
> I am trying to run the long_mris_slopes command for surfaces. It worked well 
> the thickness, but when I run it for surfaces, my terminal tells me that the 
> surface file (lh.surface or rh.surface) is missing. It appears that all my 
> subjects are missing those files. I've search the list and no similar error 
> seems to have been reported.
> 
> 
> This is the exact command I used:  long_mris_slopes --qdec 
> /Applications/freesurfer/subjects/longitudinal_training/long_training.dat 
> --meas surface --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack 
> --do-label --time weeks --qcache fsaverage --sd 
> /Applications/freesurfer/subjects/
> 
> 
> I am running a on a OS X El Captain software, and the FreeSurfer version I am 
> using is the most recent one. I also joined the recon-all.long of one of my 
> subject (of the base, since I'm running longitudinal data), in case it could 
> help.
> 
> 
> Regards,
> 
> 
> Nick
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Re: [Freesurfer] recon-all -base -all, "Word too long" error.

[Martin Reuter]

Hi Han, 

there is two things going on here. 
1. for some reasons there are small differences in the acquisition parameters 
across your time points. This usually indicates that there was a change in 
protocol wich could bias your longitudinal study (depending on what was changed 
and if this is consistent across subjects or not).
2. It seems recon-all has a problem with this many time points. The shell is 
bad at handling very long strings, I think it probably concatenates the 
individual directory names somewhere and then get’s the word overflow. I cannot 
fix that right now (and it may not even be that easy to fix at all). So I would 
recommend to select a subset of your time points (like up to 10), create the 
base and then add the remaining time points later to the existing base (there 
is —addtp or similar to do that). When you select the 10 make sure they are 
equally distributed across your 30 time points (beginning, middle, end of the 
series).

Best, Martin

> On Aug 16, 2016, at 8:54 AM, Hanbyul Cho  wrote:
> 
> Dear FreeSurfer experts,
> 
> I am FreeSurfer longitudinal processing the thirty time points data.
> When I tried the step 2 process to make a template, the process stopped with 
> an error.
> The error message as the below.
> 
> ===
> ...
> mri_diff --notallow-pix /home/Desktop/MyProject/CO30/mri/rawavg.mgz 
> /home/Desktop/MyProject/CO30/mri/rawavg.mgz 
> 
> Volumes differ in geometry row=1 col=1 diff=0.054242 (0.054242)
> 
> ***
> WARNING: Image geometries differ across time, maybe due to aquisition changes?
>  This can potentially bias a longitudinal study! Will continue in 10s.
> ***
> 
> Word too long.
> 
> 
> ==
> 
> My command line was:
> recon-all -base SET1template -tp CO01 -tp CO02 ... -tp CO30 -all
> 
> How can I fix the error?
> 
> Best wishes,
> 
> Han
> 
> 
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Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Matthieu Vanhoutte]

Hello FS's experts,

Would anyone have an advice for my problem ?

Best regards,
Matthieu

2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte :

> Dear experts,
>
> I am in trouble with two ways of computing mean intensity with
> mri_segstats.
>
> First I have used on .annot files with three different labels inside
> (SegId 1 to 3) :
>
> *mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot --i
> lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum*
>
> which give me those results:
> # ColHeaders  Index SegId NVertices Area_mm2 StructName Mean StdDev Min
> Max Range
>   1   1 2780514182.6  cluster-0018.8194
>   1.4351 6.210514.2947 8.0842
>   2   2  2321 1047.3  cluster-002   10.3661
>   1.0848 8.837512.9317 4.0942
>   3   3   552  313.1  cluster3  10.3365
>   0.4711 9.371911.8694 2.4975
>
> Second I have created on .label files containing the three segmented
> labels (SegId 1 to 3) and used this label with mri_segstats:
>
> *mri_segstats --slabel fsaverage lh lh.th23.cluster.thresh1.3.label --i
> lh.PET.fsaverage.sm10.mgh --excludeid 0 --sum lh.pet.label.sum *
>
> which give me those results:
> *# ColHeaders  Index SegId NVertices Area_mm2 StructName Mean StdDev Min
> Max Range  *
> *  1   1 3067815542.9  Seg0001 8.9637 1.4701 6.2105
>  14.2947 8.0842 *
>
> I verified if I obtained the same results with the two ways (.annot or
> .label) and everything is fine comparing NVertices, Area_mm2 but Mean in
> first way gives me (8.8194+10.3661+10.3365)/3 = 9.84066 and with .label
> file Mean = 8.9637.
>
> Did I have miss anything and how is computed mean intensity ?
>
> Many thanks in advance.
>
> Best regards,
> Matthieu
>
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Re: [Freesurfer] Subject: Re: Zero cortical thickness

[A Nunes]

Hi

I looked at the distribution areas with almost zero thickness and when
I saw they were on one hemisphere, I checked my bash script and found
out that for the left cortex it was calling the right hemisphere
areas.
However, I still have a few subjects which have zero thickness in some
areas of my parcelled atlas. This zero thickness is it caused by a
segmentation or a sphere reconstruction error/imperfection (in which
case the value should be NaN), or is it capturing a brain structural
characteristic worth to account for?

Thanks
Adonay

On Mon, Aug 15, 2016 at 3:06 PM, A Nunes  wrote:
> Hi Douglas,
>
> I meant a surface area extracted from a surface based atlas.
>
> Thanks
> Adonay
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[Freesurfer] recon-all -base -all, "Word too long" error.

[Hanbyul Cho]

Dear FreeSurfer experts,

I am FreeSurfer longitudinal processing the thirty time points data.
When I tried the step 2 process to make a template, the process stopped
with an error.
The error message as the below.

===
...
mri_diff --notallow-pix /home/Desktop/MyProject/CO30/mri/rawavg.mgz
/home/Desktop/MyProject/CO30/mri/rawavg.mgz

Volumes differ in geometry row=1 col=1 diff=0.054242 (0.054242)


***
WARNING: Image geometries differ across time, maybe due to aquisition
changes?
 This can potentially bias a longitudinal study! Will continue in
10s.

***

Word too long.


==

My command line was:
recon-all -base SET1template -tp CO01 -tp CO02 ... -tp CO30 -all

How can I fix the error?

Best wishes,

Han
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