Re: [Freesurfer] GPU/supercomputer adaptation of freesurfer?

[Morgan Hough]

External Email - Use Caution

Hi Richard,

That is a very good point. I knew it was being deprecated and there was
talk of OpenCL but I have not been keeping up. Multicore systems were
getting the most benefit from newer releases. Certainly, to run the
existing CUDA code involved making sure your sysadmin would give you the
older CUDA libs too.

Thank you for your input. I know it was a long time ago but I remember your
GTC presentation for sure.

Cheers,

-Morgan

On Thu, Dec 13, 2018 at 2:55 AM R Edgar  wrote:

> External Email - Use Caution
>
> Sorry I'm coming to this a bit late I'm not sure that the CUDA
> implementation is supported these days. I've not done much work on em_
> and ca_register since 2012; I'm not sure about the surface stream (I
> didn't do that port). Furthermore, I don't see CUDA being included in
> the new CMake build system. Some differences to the CPU stream are
> inevitable (floating point arithmetic and all that), but if the
> workflow in those binaries has changed since when I was working on
> them, then those changes may not be reflected in the GPU code.
>
> Regards,
>
> Richard
>
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Re: [Freesurfer] GPU/supercomputer adaptation of freesurfer?

[Morgan Hough]

External Email - Use Caution

Hi John,

I know others (Satra?) might have more recent experience. I used to be able
to get recon-all down to about 4 hours. OpenMP made the most difference but
the GPU code always helped if you have it running. It really depends on
whether you can get the admin to let you use the version of CUDA that
FreeSurfer uses, etc. I was also always doing TRACULA too and the FSL GPU
code is (IMO) essential. There are flags you add to recon-all to enable
these. If you are having trouble with CUDA, OpenMP definitely speeds things
up and try and stay on nodes with the most cores.

It’s not the supercomputing that you need really. Check what the
batch/queue system is there. Hopefully it’s SGE (or whatever its called
now) or something that can mimic SGE. I know I will always have to modify
the fsl_sub included in FreeSurfer to make sure this works properly but if
its something different don’t worry and just disable it. Again, this
problem normally comes up in TRACULA more than FS recon-all but you want to
write a small shell script that starts all your subjects and then wait for
it to be done. Sometimes the batch system will be where you also select the
nodes/num of cores.

Again, super-common:) Visualization is done on a local workstation unless
you have an interactive node that, well, usually is very site specific. Can
be useful as with a NVIDIA docker node on AWS if you want to see how it is
sometimes done with GPU for visualization with something like ParaView.

Hope that helps.

Cheers,

-Morgan

On Fri, Dec 7, 2018 at 6:42 AM John Absher  wrote:

> External Email - Use Caution
>
> Hi,
>
>
>
> I’m planning a freesurfer analysis of a large MRI dataset, and want to use
> the “380 GPU nodes” (and other cores/nodes) on the Palmetto Cluster (
> https://www.palmetto.clemson.edu/palmetto/userguide_palmetto_overview.html)
> to speed up the process. Since I am not a programmer, I’m hoping someone
> can give me a quick tutorial:
>
>
>
> a)  Is this going to speed up recon-all and the data analysis?
>
> b)  How much programming/expertise is required to enable freesurfer
> to take advantage of a supercomputer’s resources?
>
> c)   Has anyone done this already?
>
> d)  The Palmetto Cluster is more or less limited to command-line. As
> long as I visualize the data on another system, I assume this will not be a
> problem, right?
>
>
>
> Thanks,
>
>
>
> John R. Absher, MD
>
>
>
> jabs...@ghs.org
>
> GHS Neuroscience Associates
>
> University of South Carolina School of Medicine Greenville
>
> 864-350-6655 (mobile)
>
>
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Re: [Freesurfer] Freesurfer for canine

[Morgan Hough]

I will check with the Emory group that I know has been scanning canines.
Don't know if they are interested in the extra work to get FreeSurfer
output but since they are doing FMRI maybe they would be OK with sharing
their AMRI data.

It would be good to ask C. Destrieux on the progress with pig and sheep
pipelines as he was at the conference in Nantes last year for this but they
weren't quite ready to share their templates at that time. I'd love to know
what the status of that work is as I would guess it would be useful for
making a canine pipeline to some degree. All great model systems and
interesting points came up about the labeling across species.

Cheers,

-Morgan

On Mon, Apr 2, 2018 at 6:27 PM Douglas N. Greve 
wrote:

> To my knowledge, it does not work with canine data, but maybe someone
> has done it.
>
>
> On 04/02/2018 04:41 PM, Khoi Mai wrote:
> > Hi,
> >
> > I am interested in the automated volumetric analysis for canine. My
> > question is how can we go about adjusting the pipeline to accommodate
> > canine data.
> >
> > Thank you for your reply
> >
> > Best,
> >
> > Khoi
> >
> >
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[Freesurfer] QAtools errors with aseg QA

[Morgan Hough]

Hi there,

Just trying out the QAtools and I notice that there are a number of
(standard_in) 1: syntax error reports for each subcortical label:

checking subcortical label: Endosteum, . +/- .
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error

As best as I can tell its in some bc calculations that are being done and I
assume these errors are why there are no aseg reports made. All the other
calculations and snapshots seem to work just fine. I am running FreeSurfer
5.3 and QAtools 1.1 on Ubuntu 12.04. Thanks in advance.

Cheers,

-Morgan
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[Freesurfer] mri_convert ERROR: could not determine file

[Morgan Hough]

Hi there,

I am trying to run reg-feat2anat and having a bit of an odd problem. It runs 
but doesn't produce a anat2exf.register.dat. If I look at the 
anat2exf.register.dat.fslregister.log file I see right at the beginning it fail 
with:

/data/results/genDIS
mri_convert ERROR: could not determine file for 
/data/freesurfer_recons/HierGENDIS/WaisgenDIS600/mri/ERROR: 
/data/results/genDIS/WaisgenDIS600/gendistask_full_search.feat/reg/freesurfer/tmp/refvol.fslregister.nii
mri_convert ERROR: could not determine file for 
/data/freesurfer_recons/HierGENDIS/WaisgenDIS600/mri/ERROR: 
/data/results/genDIS/WaisgenDIS600/gendistask_full_search.feat/reg/freesurfer/tmp/refvol.fslregister.nii

mri_convert: extra arguments (not and following)

type mri_convert -u for usage

This is running on a SGE cluster using Ubuntu 12.04.1, FreeSurfer 5.3 and FSL 
5.0.4 which made me think it is is similar to Sal's problem recently. So I 
added set fsvol = brainmask and that seems to have fixed it. Is there a 
different fix I can make to solve this? 

Cheers,

-Morgan



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Re: [Freesurfer] FS 5.2-beta run-times on Amazon Web services (AWS)

[Morgan Hough]

Hi Mehul,

Thank you for sharing this. Could you include how this would compare to a GPU 
AWS instance with FreeSurfer's GPU switch?

Cheers,

-Morgan

On Feb 1, 2013, at 6:54 PM, Mehul Sampat mpsam...@gmail.com wrote:

 Hi Folks, 
 
 Just wanted to share our experience with running FS 5.2-beta on Amazon Web 
 Services (AWS). 
 Basically, AWS has multiple instance types 
 (http://aws.amazon.com/ec2/instance-types/) and we were trying to figure out 
 the most cost-effective approach. 
 
 We ran two subjects through FS 5.2-beta on M1 Large Instance (m1.large) and 
 Cluster Compute Eight Extra Large Instance (cc2.8xlarge). (same subjects run 
 on both instance). We expected cc2.8xlarge to be faster (but it is also more 
 expensive: $2.4 per hour; 8 cores); The run-times we got:
 
 instance-type  subject start-time  
 end-time  run-time
 m1.large   subject-1   01:05:44 UTC 2013  15:40:45 UTC 
 2013   ~14hr-35mins
 m1.large   subject-2   01:06:06 UTC 2013  15:08:45 UTC 
 2013   ~14hr-02mins
 cc2.8xlargesubject-1   01:26:38 UTC 2013  12:30:23 UTC 2013   
 ~11hr-04mins
 cc2.8xlargesubject-2   01:27:28 UTC 2013  12:19:08 UTC 2013   
 ~10hr-52mins
 
 Although m1.large is a few hours slower, it seems to be the more cost 
 effective option since it is $0.24 per hour (2 cores). If you have run 
 Freesurfer on AWS, do you have a similar experience ? Any suggestions to 
 speed up the run-times on AWS would be very helpful.
 
 Thanks
 Mehul
 
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[Freesurfer] Sulcal CSF measure

[Morgan Hough]

Hi there,

I was wondering if sulcal CSF differences should be reported given the 
difficulty in its identification from T1 data? How is sulcal CSF defined 
by FS? Thanks in advance for your time.


Cheers,

-Morgan
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[Freesurfer] High-resolution limits of FS4

[Morgan Hough]

Hi there,

I just wanted to check on the spatial resolution limits of FS4. Is it 
possible to process a whole-brain, 0.5mm isotropic voxel size volume 
without downsampling it? Thanks in advance.


Cheers,

-Morgan
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[Freesurfer] Banks of the superior temporal sulcus question

[Morgan Hough]

I was just wondering why the banks of the superior temporal sulcus was 
made into its own label on the Desikan template. Does this correspond 
(roughly) to a particular functional area. I didn't see anything in the 
paper about why it was chosen. Is it just easy to define given 
sulcal/gyral boundaries? Thanks in advance.


Cheers,

-Morgan
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Re: [Freesurfer] Banks of the superior temporal sulcus question

[Morgan Hough]

Hi Bruce,

I see. It just seems to be surrounded by very large parcellation units 
that haven't been divided. Does it have good landmarks to place it along 
the sulcus?


Cheers,

-Morgan

Bruce Fischl wrote:
I think it's where Ron Killiany previously found large effects in 
prodromal AD.


On Mon, 6 Aug 2007, Morgan Hough wrote:

I was just wondering why the banks of the superior temporal sulcus 
was made into its own label on the Desikan template. Does this 
correspond (roughly) to a particular functional area. I didn't see 
anything in the paper about why it was chosen. Is it just easy to 
define given sulcal/gyral boundaries? Thanks in advance.


Cheers,

-Morgan
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[Freesurfer] mris_anatomical_stats question

[Morgan Hough]

I am reporting thickness values from subjects native space constrained 
by mask labels using mris_anatomical_stats. I am currently getting the 
average of the unsmoothed estimates. I would like to be able to get 
smoothed values but the usage reports the smoothing option as -nsmooth 
# where the # is the # of smoothing iterations. If we are using 10mm 
FWHM smoothing for the group results can I estimate the number of 
smoothing iterations to obtain something equivalent? Would it be easier 
to use mri_surf2surf and create a  smoothed thickness file for each 
subject? Thanks again.


Cheers,

-Morgan
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[Freesurfer] mri_segstats question

[Morgan Hough]

Hi ,

I would like to use mri_segstats with an aprac parcellation to get the 
mean/stddev of the norm.mgz intensities by parcel. I have tried the 
following usage:


mri_segstats --annot con_2304 lh aparc --ctab-default --nonempty 
--excludeid 0 --sum con_2304.norm.aseg.sum --in 
$SUBJECTS_DIR/con_2304/mri/norm.mgz


but I get the same output in the sum file with either the norm or 
orig.mgz file. Also there are certain parcellation units (PU) that have 
zero mean and zero standard deviation with either input. Is this usage 
correct for the job? Thanks in advance.


Cheers,

-Morgan
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Re: [Freesurfer] Partitioning GM/WM boundary surface

[Morgan Hough]

Thanks Bruce,

From the ReconAllDevTable I see

mris_make_surfaces -mgz -w 0 -T1 brainfinalsurfs.mgz $subject $hemi

which will produce new ?h.thickness, area, curv, white and pial surfaces 
as well. Are these the options I should rerun with?


Cheers,

-Morgan

Bruce Fischl wrote:
rerun mris_make_surfaces and it will create them (and not deform the 
surface in regions outside the label)

On Wed, 25 Jul 2007, Morgan Hough wrote:


Hi Bruce,

These subjects were run with an older version of FreeSurfer and don't 
have ?h.cortex.label. I am afraid I don't see a generating command in 
the ReconAllDevTable. In ReconAllFilesVsSteps it looks like it is 
coming from mris_make_surfaces. Can I generate these labels from the 
old recon-all output?


Cheers,

-Morgan

Bruce Fischl wrote:

Hi Morgan,

yes, that seems reasonable. You can start with the ?h.cortex.label 
and subdivide it into sulcal and gyral to avoid the medial wall.


cheers,
Bruce
On Tue, 24 Jul 2007, Morgan Hough wrote:

I would like to obtain a ratio of gyral/sulcal GM/WM boundary 
surface area. I was wondering if the best solution would be to 
threshold each subject's ?h.sulc files to form a label that 
contains all gyral areas and then use mris_anatomical_stats -l to 
constrain a surface area measurement to this label? I was also 
wondering if there is a simple way to exclude the medial wall area 
from consideration in these calculations? Thanks in advance for 
your time.


Cheers,

-Morgan


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Re: [Freesurfer] mris_wm_volume

[Morgan Hough]

Hi Bruce,

I am afraid the zero is all the output I get. Do I need an updated 
mris_volume as well perhaps?


Cheers,

-Morgan

Bruce Fischl wrote:

that looks like the correct usage. Can you send the entire screen output?
On Fri, 20 Jul 2007, Morgan Hough wrote:


Hi Nick,

Thanks for the tool. I am getting output of 0 with


mris_wm_volume con_2304 lh

0

This follows the usage as I see it. Am I using this wrong?

Cheers,

-Morgan

Nick Schmansky wrote:

Morgan,

I've posted mris_wm_volume for the various platforms at this location:

  ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev

Nick

On Thu, 2007-07-19 at 17:56 +0100, Morgan Hough wrote:

Would it be possible to post binaries of mris_wm_volume again? I 
believe this is the preferred tool to calculate the total white 
matter volume over the current aseg output. Thanks in advance.


Cheers,

-Morgan

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Re: [Freesurfer] calculation of total cortical gray matter volume

[Morgan Hough]

Hi Bruce,

Our subjects don't have this label (?h.cortex) in their label 
directories. Was this introduced with a recent version? What is the best 
approximation of this cortical gray matter volume measure for people who 
have older recons?


Cheers,

-Morgan

Hi Mike,


you need to exclude non-cortical regions (e.g. hippocampus) from the 
pial volume. I think mris_anatomical_stats -l 
$subject/label/$hemi.cortex should be the right measure.


cheers,
Bruce



On Fri, 20 Apr 2007, Michael Harms wrote:

   Hello FS-list,

   Could you please confirm the recommended current approach for
   calculating the total cortical gray matter volume.

   Based on the following Wiki page
   http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats?
   action=highlightvalue=mris_volume
   I presume that the recommended calculation (illustrated using tcsh
   syntax) is:

   @ total_cort_gm_vol = `mris_volume ?h.pial` - `mris_volume ?h.white`

   My only hesitation is that I noticed the resulting value doesn't quite
   match the value of total gray matter volume that is output by
   mris_anatomical_stats.  Is this because mris_anatomical_stats uses a
   older approach that is no longer considered quite as accurate?

   thanks,
   Mike Harms



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[Freesurfer] Combining annots?

[Morgan Hough]

I have a question about using labels from different annots. The Desikan 
annot has a large region labeled unknown including medial wall and 
lateral insula and operculum. The Destrieux annot has a separate medial 
wall label. Is there an easy way to use the Destrieux annot label of the 
medial wall to subdivide the Desikan unknown label? Just trying to think 
of some way to do this without dividing the unknown label by hand for 
each subject. Thanks in advance.


Cheers,

-Morgan
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Re: [Freesurfer] mris_wm_volume

[Morgan Hough]

Morning Bruce,

I just checked this on a subject you already have there. I get the same 
result at NMR with this subject using the dev version of mris_wm_volume 
from /usr/local/freesurfer/dev/bin/mris_wm_volume which I think is the 
best match for the binary I have.


The subject is located at NMR at /autofs/homes/010/morgan/con_2878.

Cheers,

-Morgan

Bruce Fischl wrote:

works for me. Can you drop the subjects on our site?
On Tue, 24 Jul 2007, Morgan Hough wrote:


Hi Bruce,

I am afraid the zero is all the output I get. Do I need an updated 
mris_volume as well perhaps?


Cheers,

-Morgan

Bruce Fischl wrote:
that looks like the correct usage. Can you send the entire screen 
output?

On Fri, 20 Jul 2007, Morgan Hough wrote:


Hi Nick,

Thanks for the tool. I am getting output of 0 with


mris_wm_volume con_2304 lh

0

This follows the usage as I see it. Am I using this wrong?

Cheers,

-Morgan

Nick Schmansky wrote:

Morgan,

I've posted mris_wm_volume for the various platforms at this 
location:


  ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev

Nick

On Thu, 2007-07-19 at 17:56 +0100, Morgan Hough wrote:

Would it be possible to post binaries of mris_wm_volume again? I 
believe this is the preferred tool to calculate the total white 
matter volume over the current aseg output. Thanks in advance.


Cheers,

-Morgan

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[Freesurfer] corpus callosum

[Morgan Hough]

I was wondering if I can use the surface area estimate of the aparc 
corpus callosum label as a decent subject specific measurement of its 
cross-sectional area. Thanks in advance.


Cheers,

-Morgan
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Re: [Freesurfer] corpus callosum

[Morgan Hough]

Hi Bruce,

Would you believe results based on the current labels or do I need to 
wait for the new version?


Cheers,

-Morgan

Bruce Fischl wrote:

Hi Morgan,

we have explicit labeling of the cc that is more accurate that will be 
included in the upcoming release.

Bruce


On Tue, 24 Jul 2007, Morgan Hough wrote:

I was wondering if I can use the surface area estimate of the aparc 
corpus callosum label as a decent subject specific measurement of its 
cross-sectional area. Thanks in advance.


Cheers,

-Morgan
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Re: [Freesurfer] mris_wm_volume

[Morgan Hough]

Hi Bruce,

That did it. Great. The output is mm^3? Thanks again.

Cheers,

-Morgan

Bruce Fischl wrote:
oops, there should only be one --in_center on the cmd line (followed 
by 0 0 0 )

On Tue, 24 Jul 2007, Morgan Hough wrote:


Hi Bruce,

I try this in $subject/mri but I get the following:

mri_convert --in_center --in_center 0 0 0 aseg.mgz aseg_test.mgz

mri_convert: error converting --in_center to a float for 
--in_center flag


type mri_convert -u for usage

Do I need to set the output datatype with -odt uchar or something 
like that?


Cheers,

-Morgan

Bruce Fischl wrote:

okay, I think I know what's happing. Try this and see if it fixes it:

from the subject's mri dir

mri_convert --in_center --in_center 0 0 0 aseg.mg aseg_test.mgz

then run

mris_wm_volume -aseg aseg_test.mgz $subject $hemi


On Tue, 24 Jul 2007, Morgan Hough wrote:


Morning Bruce,

I just checked this on a subject you already have there. I get the 
same result at NMR with this subject using the dev version of 
mris_wm_volume from /usr/local/freesurfer/dev/bin/mris_wm_volume 
which I think is the best match for the binary I have.


The subject is located at NMR at /autofs/homes/010/morgan/con_2878.

Cheers,

-Morgan

Bruce Fischl wrote:

works for me. Can you drop the subjects on our site?
On Tue, 24 Jul 2007, Morgan Hough wrote:


Hi Bruce,

I am afraid the zero is all the output I get. Do I need an 
updated mris_volume as well perhaps?


Cheers,

-Morgan

Bruce Fischl wrote:
that looks like the correct usage. Can you send the entire 
screen output?

On Fri, 20 Jul 2007, Morgan Hough wrote:


Hi Nick,

Thanks for the tool. I am getting output of 0 with


mris_wm_volume con_2304 lh

0

This follows the usage as I see it. Am I using this wrong?

Cheers,

-Morgan

Nick Schmansky wrote:

Morgan,

I've posted mris_wm_volume for the various platforms at this 
location:


  
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev 



Nick

On Thu, 2007-07-19 at 17:56 +0100, Morgan Hough wrote:

Would it be possible to post binaries of mris_wm_volume 
again? I believe this is the preferred tool to calculate the 
total white matter volume over the current aseg output. 
Thanks in advance.


Cheers,

-Morgan

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[Freesurfer] Partitioning GM/WM boundary surface

[Morgan Hough]

I would like to obtain a ratio of gyral/sulcal GM/WM boundary surface 
area. I was wondering if the best solution would be to threshold each 
subject's ?h.sulc files to form a label that contains all gyral areas 
and then use mris_anatomical_stats -l to constrain a surface area 
measurement to this label? I was also wondering if there is a simple way 
to exclude the medial wall area from consideration in these 
calculations? Thanks in advance for your time.


Cheers,

-Morgan


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Re: [Freesurfer] mris_wm_volume

[Morgan Hough]

Hi Nick,

Thanks for the tool. I am getting output of 0 with

mris_wm_volume con_2304 lh
0

This follows the usage as I see it. Am I using this wrong?

Cheers,

-Morgan

Nick Schmansky wrote:

Morgan,

I've posted mris_wm_volume for the various platforms at this location:

  ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev

Nick

On Thu, 2007-07-19 at 17:56 +0100, Morgan Hough wrote:
  
Would it be possible to post binaries of mris_wm_volume again? I believe 
this is the preferred tool to calculate the total white matter volume 
over the current aseg output. Thanks in advance.


Cheers,

-Morgan

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[Freesurfer] another mri_vol2surf question

[Morgan Hough]

Hi there,

Hopefully a quick question. I was wondering what the del represents in 
the mri_vol2surf option --projfrac-avg?


--projfrac-avg min max del

If I use 0 and 1 for min and max, what should del be to average across 
all the voxels between the two surfaces? Thanks in advance.


Cheers,

-Morgan

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Re: [Freesurfer] another mri_vol2surf question

[Morgan Hough]

Hi Doug,

Missed it in the help. Thanks.

Cheers,

-Morgan

Doug Greve wrote:


It should be in the help (reprinted below). Smaller delta is better
but takes longer. With big functional voxels, I would not agonize too
much over making delta real small as you'll just hit the same voxel
multiple times. .25 is probably sufficient.

doug

  --projfrac-avg min max delta
  --projdist-avg min max delta

Same idea as --projfrac and --projdist, but sample at each of the
pointsbetween min and max at a spacing of delta. The samples 
are then

averagedtogether. The idea here is to average along the normal.





On Thu, 5 Jul 2007, Morgan Hough wrote:


Hi there,

Hopefully a quick question. I was wondering what the del represents 
in the mri_vol2surf option --projfrac-avg?


--projfrac-avg min max del

If I use 0 and 1 for min and max, what should del be to average 
across all the voxels between the two surfaces? Thanks in advance.


Cheers,

-Morgan

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Re: [Freesurfer] Making labels from the commandline

[Morgan Hough]

Thanks Doug,

I am having some trouble downloading this but the tksurfer interface 
suffices for now.


I would still be interested in making a label from a volumetric 
projection as this is something I can foresee being useful for other 
things as well. Is there anyway to do this after a mri_vol2surf 
projection? I would want to set a threshold and have anything above that 
threshold be made into a label for that surface.


Cheers,

-Morgan

Doug Greve wrote:


I have a relatively new program that does this.  Actually, it is an 
old program with a cryptic name (mri_cor2label). I've put a new 
(linux) version here:


ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_cor2label

See the help.

I don't know why mri_mergelabels does not work. Is it possible that 
the tail command is platform dependent?


doug



Morgan Hough wrote:

Hi Bruce,

I have been using mri_vol2surf to project nifti volumes onto subject 
surfaces but I am not sure I understand how to then convert the ouput 
.mgh file into a label that can then be used to sample the surface 
measures of that subject. I have attached an image of one subject 
(con_2304_roi_lh_lat.tif) with one volumetric ROI projected to the 
surface. As you can see it contains perhaps three patches that I 
would like to treat as one label with which I could then use to 
sample the surface measures of the subject. Is this something I can 
do with mri_vol2surf?


If I draw three labels on that subjects' surface, how do you then 
merge those labels together to be able to sample from the combined 
area? I have tried mri_mergelabel but I get a tail error when I try 
this:


mri_mergelabels -i ./lh.it-sts.roi.label -i ./lh.it.roi.label -o 
lh.combo-it.label

tail: cannot open `+3' for reading: No such file or directory
tail: cannot open `+3' for reading: No such file or directory
Done

Cheers,

-Morgan

Bruce Fischl wrote:

Hi Morgan,

what format is your volume ROI in? I think Doug's mri_vol2surf will 
do this. If you have it in our label format file, then just loading 
it into tksurfer will work if all the vertex #s are -1 (it will 
sample it onto the surface)


Bruce
On Thu, 24 May 2007, Morgan Hough wrote:

I was wondering if I can make a cortical label from a volume ROI 
from the commandline. I would like to extract thickness values from 
a region defined in each subject's volume space. Thanks in advance.


Cheers,

-Morgan
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MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

  


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Re: [Freesurfer] Making labels from the commandline

[Morgan Hough]

Hi Doug,

Thanks for the ftp fix. I have downloaded these fine now.

I don't see a use case for making a label in mri_binarize's help. When I 
project the volumes to surfaces I actually save them as nifti files so I 
can keep using avwmaths++ when I want to. What I think I am missing now 
is the way to make that into a label file that I can then use to 
constrain mris_anatomical_stats to a particular patch of the cortical 
ribbon. Can mri_binarize produce such a file? Is there something I can 
feed its output into that would accomplish that?


Cheers,

-Morgan

Doug Greve wrote:
Sorry, should be accessible now. To do what you need, you can just run 
mri_binarize on the output (or input) of vol2surf. I've put an 
uptodate copy of mri_binarize there too.


doug

Morgan Hough wrote:


Thanks Doug,

I am having some trouble downloading this but the tksurfer interface 
suffices for now.


I would still be interested in making a label from a volumetric 
projection as this is something I can foresee being useful for other 
things as well. Is there anyway to do this after a mri_vol2surf 
projection? I would want to set a threshold and have anything above 
that threshold be made into a label for that surface.


Cheers,

-Morgan

Doug Greve wrote:



I have a relatively new program that does this.  Actually, it is an 
old program with a cryptic name (mri_cor2label). I've put a new 
(linux) version here:


ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_cor2label 



See the help.

I don't know why mri_mergelabels does not work. Is it possible that 
the tail command is platform dependent?


doug



Morgan Hough wrote:


Hi Bruce,

I have been using mri_vol2surf to project nifti volumes onto 
subject surfaces but I am not sure I understand how to then convert 
the ouput .mgh file into a label that can then be used to sample 
the surface measures of that subject. I have attached an image of 
one subject (con_2304_roi_lh_lat.tif) with one volumetric ROI 
projected to the surface. As you can see it contains perhaps three 
patches that I would like to treat as one label with which I could 
then use to sample the surface measures of the subject. Is this 
something I can do with mri_vol2surf?


If I draw three labels on that subjects' surface, how do you then 
merge those labels together to be able to sample from the combined 
area? I have tried mri_mergelabel but I get a tail error when I try 
this:


mri_mergelabels -i ./lh.it-sts.roi.label -i ./lh.it.roi.label -o 
lh.combo-it.label

tail: cannot open `+3' for reading: No such file or directory
tail: cannot open `+3' for reading: No such file or directory
Done

Cheers,

-Morgan

Bruce Fischl wrote:


Hi Morgan,

what format is your volume ROI in? I think Doug's mri_vol2surf 
will do this. If you have it in our label format file, then just 
loading it into tksurfer will work if all the vertex #s are -1 (it 
will sample it onto the surface)


Bruce
On Thu, 24 May 2007, Morgan Hough wrote:

I was wondering if I can make a cortical label from a volume ROI 
from the commandline. I would like to extract thickness values 
from a region defined in each subject's volume space. Thanks in 
advance.


Cheers,

-Morgan
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[EMAIL PROTECTED]
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Re: [Freesurfer] Making labels from the commandline

[Morgan Hough]

Hi Doug,

I see what you mean now. mri_cor2label should do it. Thanks again.

Cheers,

-Morgan

Doug Greve wrote:
No, use mri_cor2label to create the label file. I think the 2nd 
example matches what you want to do.


doug

Morgan Hough wrote:


Hi Doug,

Thanks for the ftp fix. I have downloaded these fine now.

I don't see a use case for making a label in mri_binarize's help. 
When I project the volumes to surfaces I actually save them as nifti 
files so I can keep using avwmaths++ when I want to. What I think I 
am missing now is the way to make that into a label file that I can 
then use to constrain mris_anatomical_stats to a particular patch of 
the cortical ribbon. Can mri_binarize produce such a file? Is there 
something I can feed its output into that would accomplish that?


Cheers,

-Morgan

Doug Greve wrote:

Sorry, should be accessible now. To do what you need, you can just 
run mri_binarize on the output (or input) of vol2surf. I've put an 
uptodate copy of mri_binarize there too.


doug

Morgan Hough wrote:


Thanks Doug,

I am having some trouble downloading this but the tksurfer 
interface suffices for now.


I would still be interested in making a label from a volumetric 
projection as this is something I can foresee being useful for 
other things as well. Is there anyway to do this after a 
mri_vol2surf projection? I would want to set a threshold and have 
anything above that threshold be made into a label for that surface.


Cheers,

-Morgan

Doug Greve wrote:



I have a relatively new program that does this.  Actually, it is 
an old program with a cryptic name (mri_cor2label). I've put a new 
(linux) version here:


ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_cor2label 



See the help.

I don't know why mri_mergelabels does not work. Is it possible 
that the tail command is platform dependent?


doug



Morgan Hough wrote:


Hi Bruce,

I have been using mri_vol2surf to project nifti volumes onto 
subject surfaces but I am not sure I understand how to then 
convert the ouput .mgh file into a label that can then be used to 
sample the surface measures of that subject. I have attached an 
image of one subject (con_2304_roi_lh_lat.tif) with one 
volumetric ROI projected to the surface. As you can see it 
contains perhaps three patches that I would like to treat as one 
label with which I could then use to sample the surface measures 
of the subject. Is this something I can do with mri_vol2surf?


If I draw three labels on that subjects' surface, how do you then 
merge those labels together to be able to sample from the 
combined area? I have tried mri_mergelabel but I get a tail error 
when I try this:


mri_mergelabels -i ./lh.it-sts.roi.label -i ./lh.it.roi.label -o 
lh.combo-it.label

tail: cannot open `+3' for reading: No such file or directory
tail: cannot open `+3' for reading: No such file or directory
Done

Cheers,

-Morgan

Bruce Fischl wrote:


Hi Morgan,

what format is your volume ROI in? I think Doug's mri_vol2surf 
will do this. If you have it in our label format file, then just 
loading it into tksurfer will work if all the vertex #s are -1 
(it will sample it onto the surface)


Bruce
On Thu, 24 May 2007, Morgan Hough wrote:

I was wondering if I can make a cortical label from a volume 
ROI from the commandline. I would like to extract thickness 
values from a region defined in each subject's volume space. 
Thanks in advance.


Cheers,

-Morgan
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[EMAIL PROTECTED]
Phone Number: 617-724-2358 Fax: 617-726-7422

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[Freesurfer] metric distortion questions

[Morgan Hough]

Hi there,

I would like to ask some questions about metric distortion.

1. Following the Wisco et al (2007) paper, metric distortion is defined as

Metric Distortion = k * area of a triangle on a registered sphere / area 
of triangle on gray/white interface surface


which I believe I can compute using

mris_jacobian $subject/surf/lh.sphere $subject/surf/lh.sphere.reg 
$subject/surf/lh.sphere.reg.jacobian


The subject 's ?h.sphere.reg is formed from the registration of the 
inflated sphere of the subject with the Desikan et al. (2006) 40 subject 
template? From the wiki, I think the command is


mris_register -curv ?h.sphere 
$FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif 
?h.sphere.reg


so the jacobian measure is derived from the parcellation stage (stage3) 
of recon-all.


2. I would like to extract the k factor for each subject which is 
defined as


k = total surface area of original gray/white interface surface / total 
surface area of individual sphere


do I compute this from the total surface area field of

mris_anatomical_stats $subject $hemi orig / mris_anatomical_stats 
$subject $hemi sphere


or do I need to use outputs from different surfaces or extract either 
value differently? The sphere values look rather uniform and I wanted to 
check if I am using the right thing.


3. Finally, I see in the study average make_average_surface.log file:

setting group surface area to be 1142.0 cm^2 (scale=1.29)

and I was wondering what the scale factor represented here.

Thanks in advance for your time.

Cheers,

-Morgan

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Re: [Freesurfer] metric distortion questions

[Morgan Hough]

Hi Bruce,

Thanks for your email. We are actually interested in looking at k though 
and I was wondering what surfaces you use for the numerator and denominator.


Cheers,

-Morgan

Bruce Fischl wrote:

Hi Morgan,

I think mris_jacobian computes and applies the scale factor for you. 
The group average surface area is the average surface area of the 
individuals that went into the group, since the average subject has 
less surface area than any of the individuals. Doug uses this to 
compute the proper cluster sizes, but it shouldn't matter for the 
jacobian analysis.


cheers,
Bruce


On Tue, 26 Jun 2007, Morgan Hough wrote:


Hi there,

I would like to ask some questions about metric distortion.

1. Following the Wisco et al (2007) paper, metric distortion is 
defined as


Metric Distortion = k * area of a triangle on a registered sphere / 
area of triangle on gray/white interface surface


which I believe I can compute using

mris_jacobian $subject/surf/lh.sphere $subject/surf/lh.sphere.reg 
$subject/surf/lh.sphere.reg.jacobian


The subject 's ?h.sphere.reg is formed from the registration of the 
inflated sphere of the subject with the Desikan et al. (2006) 40 
subject template? From the wiki, I think the command is


mris_register -curv ?h.sphere 
$FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif 
?h.sphere.reg


so the jacobian measure is derived from the parcellation stage 
(stage3) of recon-all.


2. I would like to extract the k factor for each subject which is 
defined as


k = total surface area of original gray/white interface surface / 
total surface area of individual sphere


do I compute this from the total surface area field of

mris_anatomical_stats $subject $hemi orig / mris_anatomical_stats 
$subject $hemi sphere


or do I need to use outputs from different surfaces or extract either 
value differently? The sphere values look rather uniform and I wanted 
to check if I am using the right thing.


3. Finally, I see in the study average make_average_surface.log file:

setting group surface area to be 1142.0 cm^2 (scale=1.29)

and I was wondering what the scale factor represented here.

Thanks in advance for your time.

Cheers,

-Morgan

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Re: [Freesurfer] mri_vol2surf question

[Morgan Hough]

Hey Doug,

Sorry, what I meant was between the left and right surfaces like in the 
image that I attached.


Cheers,

-Morgan

Doug Greve wrote:
What do you mean by between the average surfaces? Between the white 
and pial? There are various projection options, eg, you can average 
between them or take the max. This type of comparison is always a bit 
ill-posed because the surface in a 3d talairach imbedding space is not 
that meaningful. You might try mapping your surface-based results into 
the talairach volume.


doug

Morgan Hough wrote:


Hi Doug,

Multiple versions are always a concern since we have multiple 
platforms but I have checked them all and I get


$Id: mri_vol2surf.c,v 1.26 2006/02/09 16:31:29 greve Exp $

on all platforms.

I think my problems with the actual output now are due to the 
problems of trying to project MNI group results onto the average 
surface - sometimes the results fall between the average surfaces. 
When viewed in tkmedit you can see why it is not mapping all the MNI 
group results to the surface. Do you think any projection distance 
changes would make sense to get a rough approx. of what the t-stats 
are closest to in this case?


Cheers,

-Morgan

Doug Greve wrote:




Morgan Hough wrote:


Hi Nick,

The file looks fine in mri_info and it is convertible to mgz. If I 
convert it to Analyze (which I can view using fslview) the 
mri_vol2surf command works. Happy to send the files along if they 
would be helpful.



Hmmm, that's strange. It's not a float2int issue. It's having 
problems opening that file. It is strange because it uses exactly 
the same code that mri_info and mri_convert use to open it. Is is 
possible that you have mixed versions? Maybe the vol2surf version 
you have is older?




I was trying to get a rough approximation of MNI152 space group 
results projected onto the average surface by registering the 
volumetric group results with FS's mni305 template and using an 
identity reg.dat as the srcreg. I have done this but the results 
look wrong. I have checked the registration of the group results to 
the mni305 template. Is there anything else I could check? Should I 
be doing this differently?



That sounds correct. If the reg looks ok, then you can load your t 
map onto fsaverage in tkmedit along with the surfaces and see 
whether they intersect your activation.


doug



Cheers,

-Morgan

Nick Schmansky wrote:


Morgan,

I'm not so sure this is a float2int problem (but Doug may be able to
answer when he gets back next week).  Can you read that .nii.gz file
with mri_info?  Can you convert it to, say, an .mgz file using
mri_convert?  The error message looks like it can't interpret the 
file

as a NIFTI file (the preceeding float2int message being misleading in
this instance, I think).

Nick


On Tue, 2007-05-29 at 23:27 +0100, Morgan Hough wrote:
 


Hi there,

I am trying to interpolate a volume of tstats to the average 
surface with mri_vol2surf but I am getting the error below. Does 
mri_vol2surf take all the inputs that mri_convert takes? Is this 
a float2int problem mentioned in the bugs section of the --help? 
If the latter, what argument should I specify with --float2int? 
Thanks in advance for your time.


Cheers,

-Morgan

mri_vol2surf --src vbm_results_mni305_tl.nii.gz --trgsubject 
average --hemi lh --surf inflated --surfreg lh.sphere.reg --out 
lh.vbm_surf_results.mgh --srcreg reg.dat

srcvol = vbm_results_mni305_tl.nii.gz
srcreg = reg.dat
srcregold = 0
srcwarp unspecified
surf = inflated
hemi = lh
trgsubject = average
surfreg = lh.sphere.reg
interp = nearest
float2int = round
INFO: float2int code = 2
niiRead(): error opening file 
/home/fs11/mhough/Research/SOS/vbm_interp_results/vbm_results_mni305_tl.nii.gz 


ERROR: could not read vbm_results_mni305_tl.nii.gz as type 24
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Re: [Freesurfer] mri_vol2surf question

[Morgan Hough]

Hi Nick,

The file looks fine in mri_info and it is convertible to mgz. If I 
convert it to Analyze (which I can view using fslview) the mri_vol2surf 
command works. Happy to send the files along if they would be helpful.


I was trying to get a rough approximation of MNI152 space group results 
projected onto the average surface by registering the volumetric group 
results with FS's mni305 template and using an identity reg.dat as the 
srcreg. I have done this but the results look wrong. I have checked the 
registration of the group results to the mni305 template. Is there 
anything else I could check? Should I be doing this differently?


Cheers,

-Morgan

Nick Schmansky wrote:

Morgan,

I'm not so sure this is a float2int problem (but Doug may be able to
answer when he gets back next week).  Can you read that .nii.gz file
with mri_info?  Can you convert it to, say, an .mgz file using
mri_convert?  The error message looks like it can't interpret the file
as a NIFTI file (the preceeding float2int message being misleading in
this instance, I think).

Nick


On Tue, 2007-05-29 at 23:27 +0100, Morgan Hough wrote:
  

Hi there,

I am trying to interpolate a volume of tstats to the average surface 
with mri_vol2surf but I am getting the error below. Does mri_vol2surf 
take all the inputs that mri_convert takes? Is this a float2int problem 
mentioned in the bugs section of the --help? If the latter, what 
argument should I specify with --float2int? Thanks in advance for your time.


Cheers,

-Morgan

mri_vol2surf --src vbm_results_mni305_tl.nii.gz --trgsubject average 
--hemi lh --surf inflated --surfreg lh.sphere.reg --out 
lh.vbm_surf_results.mgh --srcreg reg.dat

srcvol = vbm_results_mni305_tl.nii.gz
srcreg = reg.dat
srcregold = 0
srcwarp unspecified
surf = inflated
hemi = lh
trgsubject = average
surfreg = lh.sphere.reg
interp = nearest
float2int = round
INFO: float2int code = 2
niiRead(): error opening file 
/home/fs11/mhough/Research/SOS/vbm_interp_results/vbm_results_mni305_tl.nii.gz

ERROR: could not read vbm_results_mni305_tl.nii.gz as type 24
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[Freesurfer] mri_vol2surf question

[Morgan Hough]

Hi there,

I am trying to interpolate a volume of tstats to the average surface 
with mri_vol2surf but I am getting the error below. Does mri_vol2surf 
take all the inputs that mri_convert takes? Is this a float2int problem 
mentioned in the bugs section of the --help? If the latter, what 
argument should I specify with --float2int? Thanks in advance for your time.


Cheers,

-Morgan

mri_vol2surf --src vbm_results_mni305_tl.nii.gz --trgsubject average 
--hemi lh --surf inflated --surfreg lh.sphere.reg --out 
lh.vbm_surf_results.mgh --srcreg reg.dat

srcvol = vbm_results_mni305_tl.nii.gz
srcreg = reg.dat
srcregold = 0
srcwarp unspecified
surf = inflated
hemi = lh
trgsubject = average
surfreg = lh.sphere.reg
interp = nearest
float2int = round
INFO: float2int code = 2
niiRead(): error opening file 
/home/fs11/mhough/Research/SOS/vbm_interp_results/vbm_results_mni305_tl.nii.gz

ERROR: could not read vbm_results_mni305_tl.nii.gz as type 24
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Re: [Freesurfer] Area measurement question

[Morgan Hough]

Hey Bruce,

I'll use the average of the two. Thanks.

-Morgan

Bruce Fischl wrote:
hmmm, I wrote something a while ago to generate a middle surface, but 
I'm not sure I would recommend it. It's kind of strange to be 
measuring the area of a surface that doesn't exist, isn't it? I would 
rather use the average of the two


Bruce


On Thu, 24 May 2007, Morgan Hough wrote:


Thanks Bruce,

These will give quite different values, right? Any chance of getting 
at the mid-thickness area?


Cheers,

-Morgan

Bruce Fischl wrote:

Hi Morgan,

you get to choose. I think the default ?h.area file uses the 
?h.white surface, but you can give mris_anatomical_stats whatever 
surface you want. I think we also by default compute an ?h.pial.area 
file.


Bruce
On Thu, 24 May 2007, Morgan Hough wrote:

I just wanted to check which surface was used to compute area and 
which reference would have this information. Thanks in advance.


Cheers,

-Morgan
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[Freesurfer] Making labels from the commandline

[Morgan Hough]

I was wondering if I can make a cortical label from a volume ROI from 
the commandline. I would like to extract thickness values from a region 
defined in each subject's volume space. Thanks in advance.


Cheers,

-Morgan
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[Freesurfer] Area measurement question

[Morgan Hough]

I just wanted to check which surface was used to compute area and which 
reference would have this information. Thanks in advance.


Cheers,

-Morgan
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Re: [Freesurfer] Area measurement question

[Morgan Hough]

Thanks Bruce,

These will give quite different values, right? Any chance of getting at 
the mid-thickness area?


Cheers,

-Morgan

Bruce Fischl wrote:

Hi Morgan,

you get to choose. I think the default ?h.area file uses the ?h.white 
surface, but you can give mris_anatomical_stats whatever surface you 
want. I think we also by default compute an ?h.pial.area file.


Bruce
On Thu, 24 May 2007, Morgan Hough wrote:

I just wanted to check which surface was used to compute area and 
which reference would have this information. Thanks in advance.


Cheers,

-Morgan
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[Freesurfer] quick scatterplot label question

[Morgan Hough]

Once I have defined a label in tksurfer and I select *Tools - *Group* 
- Graph Marked Vertices Avg to open a scatterplot window, how do I 
change the y axis label from the default external label. I assume that 
I need to set this beforehand in the fsgd file but I wasn't sure how. 
Thanks in advance.


Cheers,

-Morgan
*
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[Freesurfer] cortical mask for group analysis

[Morgan Hough]

I would like to make a mask for group analysis that excludes the unknown 
parcellation area. Since I would like to apply the same mask to all 
subjects (I have already brought them into alignment with mri_preproc), 
I was wondering how I can convert the average template  
label/?h.aparc.annot to a .mgz files that I could then convert into a 
mask. Is there an alternative way to produce such a mask?


As a follow-up question, I was wondering if parcellation areas such as 
the corpus callosum should also be excluded from analysis? Are the 
thickness estimates made in the corpus callosum parcellation area 
interpretable?


Thanks in advance for your time.

Cheers,

-Morgan
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Re: [Freesurfer] cortical mask for group analysis

[Morgan Hough]

Thanks Bruce,

Are there any other parcellation units that should be excluded? That 
seems to be the only white matter PU.


Cheers,

-Morgan

Bruce Fischl wrote:

Hi Morgan,

no thickness should not be used in the cc.

Bruce
On Fri, 6 Apr 2007, Morgan Hough wrote:

I would like to make a mask for group analysis that excludes the 
unknown parcellation area. Since I would like to apply the same mask 
to all subjects (I have already brought them into alignment with 
mri_preproc), I was wondering how I can convert the average template  
label/?h.aparc.annot to a .mgz files that I could then convert into a 
mask. Is there an alternative way to produce such a mask?


As a follow-up question, I was wondering if parcellation areas such 
as the corpus callosum should also be excluded from analysis? Are the 
thickness estimates made in the corpus callosum parcellation area 
interpretable?


Thanks in advance for your time.

Cheers,

-Morgan
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Re: [Freesurfer] cortical mask for group analysis

[Morgan Hough]

I am using ICA on what would be input to mri_glmfit but since ICA is 
multivariate I need to exclude regions that don't have interpretable 
thickness or distortion measures. It seems like unknown and corpus 
callosum are the two to exclude. Are there any others I should exclude?


I would like to convert the ?h.aparc.annot files to .mgz if that gets me 
surface files integer coded with the regions. That way I can binarize 
and exclude those regions with avwtools as I will need to convert to 
nifti to do the ICA analysis anyway. What would you suggest for this?


Cheers,

-Morgan

Bruce Fischl wrote:

which parcellation are you using?

On Fri, 6 Apr 2007, Morgan Hough wrote:


Thanks Bruce,

Are there any other parcellation units that should be excluded? That 
seems to be the only white matter PU.


Cheers,

-Morgan

Bruce Fischl wrote:

Hi Morgan,

no thickness should not be used in the cc.

Bruce
On Fri, 6 Apr 2007, Morgan Hough wrote:

I would like to make a mask for group analysis that excludes the 
unknown parcellation area. Since I would like to apply the same 
mask to all subjects (I have already brought them into alignment 
with mri_preproc), I was wondering how I can convert the average 
template  label/?h.aparc.annot to a .mgz files that I could then 
convert into a mask. Is there an alternative way to produce such a 
mask?


As a follow-up question, I was wondering if parcellation areas such 
as the corpus callosum should also be excluded from analysis? Are 
the thickness estimates made in the corpus callosum parcellation 
area interpretable?


Thanks in advance for your time.

Cheers,

-Morgan
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Re: [Freesurfer] cortical mask for group analysis

[Morgan Hough]

Hi Nick,

I see. I am just not sure how to put this back together again to match 
the registered thickness files in the .mgh file. Do the vertices have 
unique ids? Can I cat and sort them? Can I dump matching information 
from my particular thickness group file and then sort?


Is there someway to binarize the .annot file to use as a mask with 
mri_glmfit?


Cheers,

-Morgan

Nick Schmansky wrote:

Morgan,

If you do this:

  mri_annotation2label --subject subjid --hemi rh \
--outdir ./labels

you will get label files in the ./labels directory.  Those label files
are text files listing the vertices and x,y.z of each label, including
'unknown' and 'corpuscallosum' (which are the only two that need
excluding).  Will that provide you with what you need?

Nick

On Fri, 2007-04-06 at 21:35 +0100, Morgan Hough wrote:
  
I am using ICA on what would be input to mri_glmfit but since ICA is 
multivariate I need to exclude regions that don't have interpretable 
thickness or distortion measures. It seems like unknown and corpus 
callosum are the two to exclude. Are there any others I should exclude?


I would like to convert the ?h.aparc.annot files to .mgz if that gets me 
surface files integer coded with the regions. That way I can binarize 
and exclude those regions with avwtools as I will need to convert to 
nifti to do the ICA analysis anyway. What would you suggest for this?


Cheers,

-Morgan

Bruce Fischl wrote:


which parcellation are you using?

On Fri, 6 Apr 2007, Morgan Hough wrote:

  

Thanks Bruce,

Are there any other parcellation units that should be excluded? That 
seems to be the only white matter PU.


Cheers,

-Morgan

Bruce Fischl wrote:


Hi Morgan,

no thickness should not be used in the cc.

Bruce
On Fri, 6 Apr 2007, Morgan Hough wrote:

  
I would like to make a mask for group analysis that excludes the 
unknown parcellation area. Since I would like to apply the same 
mask to all subjects (I have already brought them into alignment 
with mri_preproc), I was wondering how I can convert the average 
template  label/?h.aparc.annot to a .mgz files that I could then 
convert into a mask. Is there an alternative way to produce such a 
mask?


As a follow-up question, I was wondering if parcellation areas such 
as the corpus callosum should also be excluded from analysis? Are 
the thickness estimates made in the corpus callosum parcellation 
area interpretable?


Thanks in advance for your time.

Cheers,

-Morgan
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Re: [Freesurfer] cortical mask for group analysis

[Morgan Hough]

Thanks Doug,

Does a mask.mgh file get written out to the glmdir?

Cheers,

-Morgan

Doug Greve wrote:


If you're using glmfit, you can --label 
$SUBJECTS_DIR/fsaverage/lh.Medial_wall.label --mask-inv




Morgan Hough wrote:


Hi Nick,

I see. I am just not sure how to put this back together again to 
match the registered thickness files in the .mgh file. Do the 
vertices have unique ids? Can I cat and sort them? Can I dump 
matching information from my particular thickness group file and then 
sort?


Is there someway to binarize the .annot file to use as a mask with 
mri_glmfit?


Cheers,

-Morgan

Nick Schmansky wrote:


Morgan,

If you do this:

  mri_annotation2label --subject subjid --hemi rh \
--outdir ./labels

you will get label files in the ./labels directory.  Those label files
are text files listing the vertices and x,y.z of each label, including
'unknown' and 'corpuscallosum' (which are the only two that need
excluding).  Will that provide you with what you need?

Nick

On Fri, 2007-04-06 at 21:35 +0100, Morgan Hough wrote:
 

I am using ICA on what would be input to mri_glmfit but since ICA 
is multivariate I need to exclude regions that don't have 
interpretable thickness or distortion measures. It seems like 
unknown and corpus callosum are the two to exclude. Are there any 
others I should exclude?


I would like to convert the ?h.aparc.annot files to .mgz if that 
gets me surface files integer coded with the regions. That way I 
can binarize and exclude those regions with avwtools as I will need 
to convert to nifti to do the ICA analysis anyway. What would you 
suggest for this?


Cheers,

-Morgan

Bruce Fischl wrote:
  

which parcellation are you using?

On Fri, 6 Apr 2007, Morgan Hough wrote:



Thanks Bruce,

Are there any other parcellation units that should be excluded? 
That seems to be the only white matter PU.


Cheers,

-Morgan

Bruce Fischl wrote:
  

Hi Morgan,

no thickness should not be used in the cc.

Bruce
On Fri, 6 Apr 2007, Morgan Hough wrote:


I would like to make a mask for group analysis that excludes 
the unknown parcellation area. Since I would like to apply the 
same mask to all subjects (I have already brought them into 
alignment with mri_preproc), I was wondering how I can convert 
the average template  label/?h.aparc.annot to a .mgz files that 
I could then convert into a mask. Is there an alternative way 
to produce such a mask?


As a follow-up question, I was wondering if parcellation areas 
such as the corpus callosum should also be excluded from 
analysis? Are the thickness estimates made in the corpus 
callosum parcellation area interpretable?


Thanks in advance for your time.

Cheers,

-Morgan
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Re: [Freesurfer] cortical mask for group analysis

[Morgan Hough]

I see this does output a mask.mgh which is just what I need. I can 
convert this and have my nifti mask. Thanks again.


Doug Greve wrote:


If you're using glmfit, you can --label 
$SUBJECTS_DIR/fsaverage/lh.Medial_wall.label --mask-inv




Morgan Hough wrote:


Hi Nick,

I see. I am just not sure how to put this back together again to 
match the registered thickness files in the .mgh file. Do the 
vertices have unique ids? Can I cat and sort them? Can I dump 
matching information from my particular thickness group file and then 
sort?


Is there someway to binarize the .annot file to use as a mask with 
mri_glmfit?


Cheers,

-Morgan

Nick Schmansky wrote:


Morgan,

If you do this:

  mri_annotation2label --subject subjid --hemi rh \
--outdir ./labels

you will get label files in the ./labels directory.  Those label files
are text files listing the vertices and x,y.z of each label, including
'unknown' and 'corpuscallosum' (which are the only two that need
excluding).  Will that provide you with what you need?

Nick

On Fri, 2007-04-06 at 21:35 +0100, Morgan Hough wrote:
 

I am using ICA on what would be input to mri_glmfit but since ICA 
is multivariate I need to exclude regions that don't have 
interpretable thickness or distortion measures. It seems like 
unknown and corpus callosum are the two to exclude. Are there any 
others I should exclude?


I would like to convert the ?h.aparc.annot files to .mgz if that 
gets me surface files integer coded with the regions. That way I 
can binarize and exclude those regions with avwtools as I will need 
to convert to nifti to do the ICA analysis anyway. What would you 
suggest for this?


Cheers,

-Morgan

Bruce Fischl wrote:
  

which parcellation are you using?

On Fri, 6 Apr 2007, Morgan Hough wrote:



Thanks Bruce,

Are there any other parcellation units that should be excluded? 
That seems to be the only white matter PU.


Cheers,

-Morgan

Bruce Fischl wrote:
  

Hi Morgan,

no thickness should not be used in the cc.

Bruce
On Fri, 6 Apr 2007, Morgan Hough wrote:


I would like to make a mask for group analysis that excludes 
the unknown parcellation area. Since I would like to apply the 
same mask to all subjects (I have already brought them into 
alignment with mri_preproc), I was wondering how I can convert 
the average template  label/?h.aparc.annot to a .mgz files that 
I could then convert into a mask. Is there an alternative way 
to produce such a mask?


As a follow-up question, I was wondering if parcellation areas 
such as the corpus callosum should also be excluded from 
analysis? Are the thickness estimates made in the corpus 
callosum parcellation area interpretable?


Thanks in advance for your time.

Cheers,

-Morgan
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[Freesurfer] recon-all error

[Morgan Hough]

I downloaded the latest freesurfer-dev and I was testing out my install
with recon-all -autorecon-all -subjid bert and I am getting this
error.

mri_convert nu4.mnc nu.mgz
mincRead(): can't find
file /var/scratch11/mhough/subjects/bert/mri/nu4.mnc
reading from nu4.mnc...
ERROR: converting nu to COR/mgz

The file certainly isn't there and I don't see anything in mri/norm if
that is where it should be. Here's what there is:

[EMAIL PROTECTED] bert]$ find . -name *.mnc
./mri/tmp-mri_motion_correct2-32472/cor-1.mnc
./mri/tmp-mri_motion_correct2-32472/cor-2.mnc
./mri/tmp-mri_motion_correct2-32472/cor-3.mnc

[EMAIL PROTECTED] bert]$ which nu_correct
/usr/local/freesurfer/lib/mni/bin/nu_correct

Just to double check it wasn't something special about bert I created a
new directory for my one subject that I want to process and I got the
same error. 

Thanks in advance.

Cheers,

-Morgan

-- 
Morgan G. Hough, DPhil Candidate
University of Oxford, Centre for Functional MRI of the Brain (FMRIB)
John Radcliffe Hospital, Headington, Oxford OX3 9DU, United Kingdom
Tel:+44 (0) 1865 222545  / Fax:  +44 (0) 1865 222717
e-mail: [EMAIL PROTECTED]  / URL:  http://www.fmrib.ox.ac.uk/~mhough


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