[Freesurfer] mri_glmfit error " FSGD file exceeds the maximum allowed 2000"

[Avram Holmes]

FreeSurfer List,

I am attempting to run an analyses on 2051 participants. However, when I reach 
the mri_glmfit stage I receive the following error. 

ERROR: gdfReadV1: the number of inputs in FSGD file exceeds the maximum allowed 
2000

Is there a work around for this? 

Thank you in advance for any help you can offer,
Avram

Avram Holmes PhD
Assistant Professor
Department of Psychology, Yale University
Email: avram.hol...@yale.edu
Office: 203-436-9240
Web: holmeslab.commons.yale.edu

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Re: [Freesurfer] Dealing with hyper-intensities

[Bruce Fischl]

Hi Cassie

those are the result of low bandwidth and susceptibility artifacts. 
There's not much that can be done about them post-hoc - the images don't 
contain enough information to reconstruct accurate models in those 
regions. In general we recommend higher bandwidth sequences for this 
reason, ideall multi-echo mprage


sorry
Bruce



On Mon, 16 Mar 2015, Cassandra Wannan wrote:



Hi guys,


I am quite new to Freesurfer and am having some issues with
hyper-intensities in the set of scans I am working on. The spots are
appearing mainly in GM in the inferior temporal lobes and the orbitofrontal
cortex, and seem to be in all of the scans I have looked at so far from my
data set (these are old 1.5T scans from the late 90's). 


I don't know if there is anything to be done about the issue, but any advice
would be greatly appreciated, particularly as both of these regions are ROIs
for my study. In some areas, it doesn't look as though the hyper-intensities
have affected the wm or pail boundaries, but in others they clearly have. 


Cheers,


Cassie

 


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[Freesurfer] [FreeSurfer] mri_glmfit with fractional values in contrast file .mtx

[Matthieu Vanhoutte]

Dear experts,

Could you indicate me how to specify a contrast vector with fractional
values ? I tried the below formats without success in the .mtx file:

[0 0 0 0 0 0 1 1 1 -1 -1 -1]/3

|0 0 0 0 0 0 1 1 1 -1 -1 -1|/3

0 0 0 0 0 0 1/3 1/3 1/3 -1/3 -1/3 -1/3

Thank in advance for helping !

Best regards,

-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France
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[Freesurfer] [FreeSurfer] Visualize & Compute Overlaps between two significant surface maps

[Matthieu Vanhoutte]

Dear FreeSurer's experts,

I used group analysis based on GLM to compute significative surface maps of
different characteristics : thickness, CBF,...

Now I've got these maps I would like to visualize overlaps between two
different maps and compute the overlap ratio.

How could I succeed these two steps ?

Best regards,

-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France
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Re: [Freesurfer] MNIX/Y/Z coordinates in mri_glmfit-sim .summary file

[Douglas N Greve]

They are MNI305 coordinates. When we mention "Talairach" coordinates, it 
refers to mni305 coordinates that have been transformed according to 
some work done by Matthew Brett. It used to be documented here 
http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html, but it is not in 
that location anymore

doug

On 03/15/2015 04:10 PM, Nicola Toschi wrote:
> Hi list,
>
> I noticed that, while the wiki refers to Talairach coordinates named
> TalX/Y/Z
> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary),
> the header in my .summary files reads something like:
>
> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWP
> CWPLowCWPHi   NVtxs   Annot
>
> could someone confirm what atlas space the MINX/MINY/MNIZ coordinates
> are in? Is it Talairach, MNI152 or something else?
>
> Thanks in advance,
>
> Nicola
>
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>

-- 
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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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Re: [Freesurfer] [FreeSurfer] mri_glmfit with fractional values in contrast file .mtx

[Douglas N Greve]

you'll need to use .33

On 03/16/2015 11:09 AM, Matthieu Vanhoutte wrote:
> Dear experts,
>
> Could you indicate me how to specify a contrast vector with fractional 
> values ? I tried the below formats without success in the .mtx file:
>
> [0 0 0 0 0 0 1 1 1 -1 -1 -1]/3
>
> |0 0 0 0 0 0 1 1 1 -1 -1 -1|/3
>
> 0 0 0 0 0 0 1/3 1/3 1/3 -1/3 -1/3 -1/3
>
> Thank in advance for helping !
>
> Best regards,
>
> -
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
>
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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
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Re: [Freesurfer] mri_glmfit error " FSGD file exceeds the maximum allowed 2000"

[Douglas N Greve]

This is hard coded unfortunately. I've bumped it up to 20k in the most 
recent version. I've put a linux version here

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit



On 03/16/2015 06:38 AM, Avram Holmes wrote:
> FreeSurfer List,
>
> I am attempting to run an analyses on 2051 participants. However, when 
> I reach the mri_glmfit stage I receive the following error.
>
> ERROR: gdfReadV1: the number of inputs in FSGD file exceeds the 
> maximum allowed 2000
>
> Is there a work around for this?
>
> Thank you in advance for any help you can offer,
> Avram
>
> Avram Holmes PhD
> Assistant Professor
> Department of Psychology, Yale University
> Email: avram.hol...@yale.edu 
> Office: 203-436-9240
> Web: holmeslab.commons.yale.edu 
>
>
>
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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
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Re: [Freesurfer] [FreeSurfer] Visualize & Compute Overlaps between two significant surface maps

[Douglas N Greve]

For visualizing the overlap, I would probably create a segmentation in 
which each vertex is either 1 (present in thickness), 2 (present in 
CBF), or 3 present in both. You can do this in matlab or with a 
combination of mri_binarize and fscalc. You can then create an 
annotation from the seg with mris_seg2annot. I would compute a dice 
coefficent of the overlap in matlab, something like

dice = n12/((n1+n2)/2)

where n1 is the number of vetices in thick, n2 for cbf, and n12 is the 
number that overlap

doug

On 03/16/2015 12:09 PM, Matthieu Vanhoutte wrote:
> Dear FreeSurer's experts,
>
> I used group analysis based on GLM to compute significative surface 
> maps of different characteristics : thickness, CBF,...
>
> Now I've got these maps I would like to visualize overlaps between two 
> different maps and compute the overlap ratio.
>
> How could I succeed these two steps ?
>
> Best regards,
>
> -
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
>
> ___
> 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] Drawing ROIs using coordinates in another space?

[Natalie Garcia]

Hi all,

I'm working with BrainVoyager and Freesurfer. I have some Talairach
coordinates from BV for a functional ROI, and I'm trying to see if I can
use these coordinates in Freesurfer to draw the same ROI on the structural
slices. Is this possible?

Alternatively, is it possible to draw a sphere ROI in Freesurfer that will
be applied to all my subjects for group-level comparisons?

Any help would be greatly appreciated!


Best,
Natalie

-- 
 Natalie V. Garcia
Graduate Fellow, Cognitive Neuroscience
Department of Psychology
The Pennsylvania State University
423 Moore Building
University Park, PA 16802
nvg...@psu.edu
http://sites.psu.edu/scherflab/
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Re: [Freesurfer] [FreeSurfer] mri_glmfit with fractional values in contrast file .mtx

[Matthieu Vanhoutte]

Thank you Douglas.

Matthieu Vanhoutte, MSc
Research Engineer - Neuroradiology Department
Regional University Hospital, Lille, France
Le 16 mars 2015 18:17, "Douglas N Greve"  a
écrit :

> you'll need to use .33
>
> On 03/16/2015 11:09 AM, Matthieu Vanhoutte wrote:
> > Dear experts,
> >
> > Could you indicate me how to specify a contrast vector with fractional
> > values ? I tried the below formats without success in the .mtx file:
> >
> > [0 0 0 0 0 0 1 1 1 -1 -1 -1]/3
> >
> > |0 0 0 0 0 0 1 1 1 -1 -1 -1|/3
> >
> > 0 0 0 0 0 0 1/3 1/3 1/3 -1/3 -1/3 -1/3
> >
> > Thank in advance for helping !
> >
> > Best regards,
> >
> > -
> > Matthieu Vanhoutte, MSc
> > Research Engineer - Department of Neuroradiology
> > Regional University Hospital, Lille, France
> >
> >
> > ___
> > 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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>
>
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Re: [Freesurfer] [FreeSurfer] Visualize & Compute Overlaps between two significant surface maps

[Matthieu Vanhoutte]

Thank you Douglas I will try this.

Matthieu Vanhoutte, MSc
Research Engineer - Neuroradiology Department
Regional University Hospital, Lille, France
Le 16 mars 2015 19:13, "Douglas N Greve"  a
écrit :

>
> For visualizing the overlap, I would probably create a segmentation in
> which each vertex is either 1 (present in thickness), 2 (present in
> CBF), or 3 present in both. You can do this in matlab or with a
> combination of mri_binarize and fscalc. You can then create an
> annotation from the seg with mris_seg2annot. I would compute a dice
> coefficent of the overlap in matlab, something like
>
> dice = n12/((n1+n2)/2)
>
> where n1 is the number of vetices in thick, n2 for cbf, and n12 is the
> number that overlap
>
> doug
>
> On 03/16/2015 12:09 PM, Matthieu Vanhoutte wrote:
> > Dear FreeSurer's experts,
> >
> > I used group analysis based on GLM to compute significative surface
> > maps of different characteristics : thickness, CBF,...
> >
> > Now I've got these maps I would like to visualize overlaps between two
> > different maps and compute the overlap ratio.
> >
> > How could I succeed these two steps ?
> >
> > Best regards,
> >
> > -
> > Matthieu Vanhoutte, MSc
> > Research Engineer - Department of Neuroradiology
> > Regional University Hospital, Lille, France
> >
> >
> > ___
> > 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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>
>
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Re: [Freesurfer] Trac-all error

[Emad Ahmadi]

Thank you so much, Zeke! That helped a lot.

Best,
Emad

> On Mar 10, 2015, at 11:43 PM, zkauf...@nmr.mgh.harvard.edu wrote:
> 
> Hello Emad,
> 
> The download page states that OSX versions of freesurfer require the user
> to download and install XQuartz onto their machine. I have updated the
> download page so it is a little more clear.
> https://surfer.nmr.mgh.harvard.edu/fswiki/Download 
> 
> 
> Also, the dev version of freesurfer is in a high degree of flux right now.
> We are undergoing compiler upgrades and other various changes to the
> build. This means I would expect the nightly builds to be unstable for the
> next couple days.
> 
> But installing XQuartz should resolve the issue you experienced below.
> 
> -Zeke
> 
> 
> 
>> Hello Anastasia,
>> 
>> I’m using the nightly-built version for Mac OS Lion; I double checked it
>> by the command freesurfer -ver and got this response:
>> 
>> You are running this version of FreeSurfer:
>> 
>>  freesurfer-Darwin-lion-dev-20150227
>> 
>> I’m using this version on Mac OS X Yosemite. I tried to re-download a
>> nightly built version, but it didn’t let me (presumably because it’s
>> workshop time). Please let me know how I should proceed.
>> 
>> Yours,
>> Emad
>> 
>>> On Mar 6, 2015, at 7:11 PM, Anastasia Yendiki
>>> mailto:ayend...@nmr.mgh.harvard.edu>> wrote:
>>> 
>>> 
>>> Hi Emad - The error is:
>>> dyld: Library not loaded: /usr/X11/lib/libGLU.1.dylib
>>> 
>>> Does the freesurfer build that you're using match the computer that
>>> you're running it on?
>>> 
>>> a.y
>>> 
>>> On Wed, 4 Mar 2015, Emad Ahmadi wrote:
>>> 
 Hello Freesurfers!
 
 I’m trying to use tracheal -prep, and I’m getting an error. Would
 you please help me with figuring out where the problem is? The log file
 is attached.
 
 Thank you very much,
 Emad
 
 
 
 Emad Ahmadi, MD
 ---
 Research Fellow
 Department of Radiology
 Massachusetts General Hospital
 Harvard Medical School
 
 25 New Chardon Street, Suite 400
 Boston, MA 02114
 Tel: 617 726 5237
 Email: e...@nmr.mgh.harvard.edu
 
>>> ___
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>>> 
>>> >> >
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>> 
> 
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[Freesurfer] segmentation

[Mauricio Anés]

Dear Freesurfer users,

Does anybody knows if the steps after the segmentation have some impact in
subcortical structures volume? If it does, how can I have this measurements
back even if I had already run recon-all?
best,

Maurício Anés
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Re: [Freesurfer] Thin Surface

[Pedro Rosa]

Hi, Bruce.
I tried several thresholds in some subjects and it seems to work reallh well. 
Thanks for the help!
However, I would like to ask whether I should determine the expert values based 
on the raw image (001.mgz) or the normalized image (T1.mgz)? I am asking this 
because I believe the normalization can change the intensity values a lot.
Thanks again,
Pedro.

> On Feb 18, 2015, at 19:58, Bruce Fischl  wrote:
> 
> can you check mri_segmet and mris_make_surfaces and see if the auto-detected 
> intensity parameters are reasonable? Things like max gray at csf border and 
> such. If not, you can set them explicitly using the expert opts - this 
> usually works
> Bruce
>> On Wed, 18 Feb 2015, Pedro Rosa - Gmail wrote:
>> 
>> Hi,
>> I am resending it once I could not find it in the archives.
>> Thanks,
>> Pedro.
>> 
>> Dear Freesurfers,
>> I am working on a 1.5T MPRAGE sample of first-episode psychosis and 
>> controls, and have found that some subjects end up having thin cortical 
>> surfaces with frequent unsegmented deep sulci. I think this was worse with 
>> FreeSurfer 5.3 than with FreeSurfer 5.1. I attached some screen shots of 
>> aparc+aseg labeling T1.mgz from a few of these subjects.
>> This seems to be a widespread cortical issue, although it was heterogeneous 
>> across subjects (some of them seemed to have the “caudal half" of both 
>> hemispheres adequately segmented), and trying to simply rerun those subjects 
>> was not very helpful. Should I manually work on them, rerun recon-all with 
>> distinct parameters, or just discard them?
>> Regards,
>> Pedro Rosa.
>> 
>> 
>> 
>> 
>> 
>> 
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[Freesurfer] Reading retinotopy output (eccentricity/polar) into Matlab in correct space for SPM

[Susan Wardle]

Hi all,

I’m new to both freesurfer and fMRI, and after reading some related posts on 
the forum I still can't complete this task so would appreciate any help or 
suggestions.

I’m trying to import the eccentricity and polar maps from a freesurfer 
retinotopy analysis into matlab. My goal is to have a matlab matrix which 
specifies the eccentricity and polar angle (or separate matrices for polar and 
ecc.) of every voxel in V1, which I can then link to my MVPA analysis (done 
with Matlab and SPM). So I also need to link the eccentricity/polar coordinates 
to the coordinates of the voxels as they are organised in SPM (as a 3D matrix 
with the location of each voxel in the matrix corresponding to its location in 
the structural MRI volume). 

So far, I’ve located the freesurfer matlab toolbox and used MRIread to read in 
the eccentricity and polar .nii.gz files. But because of my limited freesurfer 
knowledge, I'm unsure of the next step. Which of the freesurfer output 
files/variables do I actually want? I see there are real and imaginary 
components separately for the left and right hemispheres, for both eccentricity 
and polar. How can I combine these so that I end up with a 3D matrix containing 
the eccentricity (or polar) value for each voxel, with the location of the 
voxels in the 3D matrix corresponding to its location in the MRI volume (as in 
SPM)?

thanks in advance, any suggestions are very welcome

Susan
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