[Freesurfer] Export Functional Data Overlayed Onto Sphere

[Luis R. Piloto]

Hello,

I've specifically adopted Freesurfer for its ability to map a brain into a 
sphere.  I've ran a subject's structural data through the recon-all pipeline 
using the -all option.  With this reconstruction completed, I'd like to overlay 
functional data on the sphere.  More specifically, I'd like the ability to 
programmatically query a point on the sphere and get the corresponding 
activation.  Is there a reasonable way to do this within the Freesurfer 
pipeline?  I already have the ability to programmatically query my initial 
functional data, so it would suffice to get a transformation matrix from my 
structural data to the spherical coordinates.  Any thoughts/suggestions would 
be appreciated.

Regards,
Luis Piloto
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Re: [Freesurfer] Export Functional Data Overlayed Onto Sphere

[Bruce Fischl]

Hi Luis

if your functional data is mapped onto the surface (i.e. with 
mri_vol2surf) then it is already on the sphere. All the surfaces for a 
given subject's hemisphere are topologically equivalent, so you can simply 
look up the same vertex index on the ?h.sphere (for the metrically optimal 
spherical coordinate) or the ?h.sphere.reg (for the spherical coordinate 
that is in register across subjects).

cheers
Bruce


On Thu, 7 Jun 2012, Luis R. 
Piloto wrote:

> Hello,
>
> I've specifically adopted Freesurfer for its ability to map a brain into a 
> sphere.  I've ran a subject's structural data through the recon-all pipeline 
> using the -all option.  With this reconstruction completed, I'd like to 
> overlay functional data on the sphere.  More specifically, I'd like the 
> ability to programmatically query a point on the sphere and get the 
> corresponding activation.  Is there a reasonable way to do this within the 
> Freesurfer pipeline?  I already have the ability to programmatically query my 
> initial functional data, so it would suffice to get a transformation matrix 
> from my structural data to the spherical coordinates.  Any 
> thoughts/suggestions would be appreciated.
>
> Regards,
> Luis Piloto
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>
>
>
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Re: [Freesurfer] fsgd

[Marie Schneider]

I exactly tried that.

I typed:

mris_preproc --fsgd  \
--cache in thickness.fwhm.10.fsaverage \
--target fsaverage \
--hemi lh \
--out .mgh

everytime I am running this it says that my fsgd file cannot be found. So I
wonder where I have to save it so that FreeSurfer can find it.

Thanks for any help

Marie

2012/6/6 Douglas Greve 

>  Hi Marie, you have to pass it as a command-line option with --fsgd
> doug
>
>
> On 6/6/12 4:19 AM, Marie Schneider wrote:
>
> Dear FreeSurfer experts,
>
> I am trying to start mris_preproc, but unfortunately it doesn't find my
> created fsgd file. I saved it in the foulder where you can find all
> subjects data. Shall I save it somewhere else?
>
> Thanks for your help,
>
> best Marie
>
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Re: [Freesurfer] fsgd

[Douglas Greve]

Did you pass it the full path to the fsgd file, not just it's name? If 
so, please send the full command line. Also, run it with ---debug and 
send me the full terminal output.

doug

On 6/7/12 9:39 AM, Marie Schneider wrote:

I exactly tried that.

I typed:

mris_preproc --fsgd  \
--cache in thickness.fwhm.10.fsaverage \
--target fsaverage \
--hemi lh \
--out .mgh

everytime I am running this it says that my fsgd file cannot be found. 
So I wonder where I have to save it so that FreeSurfer can find it.


Thanks for any help

Marie

2012/6/6 Douglas Greve >


Hi Marie, you have to pass it as a command-line option with --fsgd
doug


On 6/6/12 4:19 AM, Marie Schneider wrote:

Dear FreeSurfer experts,

I am trying to start mris_preproc, but unfortunately it doesn't
find my created fsgd file. I saved it in the foulder where you
can find all subjects data. Shall I save it somewhere else?

Thanks for your help,

best Marie

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Re: [Freesurfer] 回复: Re: /path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory

[Anastasia Yendiki]

Hi Xiangzhen - Currently mri_convert does not support extracting gradients 
and b-values from dicom files. If you can get the gradients and b-values 
from the dicom header yourself, that's great. Save them in text files and 
enter the path in your dmrirc file.


a.y

On Thu, 7 Jun 2012, Xiangzhen Kong wrote:


Thank you very much, Anastasia.
I have checked the related mails in the list and found not me came across
this problem.
As you said, I know how I can run my data.
But I have a question. Why would we make trac-all compatible to other
scanner or acquisitions, since we can get bvecs and bval from the DICOM
header?
 
thank in advance.
 
 


Xiangzhen Kong
 
From: Anastasia Yendiki
Date: 2012-02-04 00:52
To: Xiangzhen Kong
CC: freesurfer
Subject: Re: [Freesurfer] /path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such
file or directory
 
Unless your dicoms came from the same acquisition as the default 
MGH/Siemens one, you'll have to set bvecfile and bvalfile and provide 
those files yourself.
 
On Fri, 3 Feb 2012, Xiangzhen Kong wrote:
 
> Hi all
> Now I am learning the trac-all using with DICOM data, but came across a
> problem.
> +++
> mv?f?xxx/dmri/dwi_orig_flip.mghdti.bvecs?/dmri/bvecs
> mv:燾annot爏tat燻/xxx/dmri/dwi_orig_flip.mghdti.bvecs':燦o爏uch爁ile爋r

?? ??ir

> ectory
> +++
> I check the dir /xxx/dmri/ and there are only two files
> 'dwi_orig_flip.nii.gz' , 'dwi_orig.nii.gz'?and a dir 'xfms'.
> Does trac-all extract bvals/bvecs automatically when start with DICOM dat
a?
> My data is from a siemens scanner.
> ?
> Thanks!
> ?
> Xiangzhen
> ?
> 2012-02-03
> 
> _
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> 
>
 
 
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Re: [Freesurfer] Mris_anatomical_stats: smoothing does not work with surface area maps

[Douglas N Greve]

Use "--sval lh.area". Also, why do you want to smooth it before 
averaging over the ROI?
doug

On 06/07/2012 01:29 AM, Jürgen Hänggi wrote:
> Hi Doug
>
> This is my command line:
>
> mris_anatomical_stats -a area_left_significant_labels.annot -t lh.area
> -nsmooth 15 -f $s/stats/lh.aparc.a2005s.stats $s lh
>
> In the past, you recommended smoothing the data with mri_surf2surf instead
> of with mris_anatomical_stats.
>
> For that purpose, I run the following command:
>
> mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval
> lh.area.15.mgh --cortex
>
> But the following error occurred:
>
> [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi%
> foreach s ( MOREA_* )
> foreach? mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval
> lh.area.15.mgh --cortex
> foreach? end
> srcsubject = MOREA_KG002
> srcval = (null)
> srctype=
> trgsubject = MOREA_KG002
> trgval = lh.area.15.mgh
> trgtype=
> srcsurfreg = sphere.reg
> trgsurfreg = sphere.reg
> srchemi= lh
> trghemi= lh
> frame  = 0
> fwhm-in= 0
> fwhm-out   = 15
> label-src  = (null)
> label-trg  = lh.cortex.label
> OKToRevFaceOrder  = 1
> Reading source surface reg
> /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.sphere.reg
> Loading source data
> Reading surface file
> /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area
> nquads=9895939,  nvertices=399
> ERROR: MRISread: file
> '/Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area' has many more
> faces than vertices!
> Probably trying to use a scalar data file as a surface!
>
> Thanks for help in advance
> Cheers
> Jürgen
>
> On [DATE], "Douglas Greve"<[ADDRESS]>  wrote:
>
>> what is your command line?
>> doug
>>
>> On 6/6/12 5:25 AM, Jürgen Hänggi wrote:
>>> Dear FS experts
>>>
>>> I have done group comparisons wrt thickness and surface area. The
>>> found clusters were written out as annotations, transformed into each
>>> individual space, and then the corresponding values were extracted.
>>>
>>> When using mris_anatomical_stats, values are different for thickness maps
>>> depending whether I used the --nsmooth 15 option or not. So good
>>> so far.
>>>
>>> However, when using the same command (see below) for ?h.area files,
>>> extracted values are the same whether or not I used the --nsmooth option.
>>>
>>> It seems that the --nsmooth option in mris_anatomical_stats does not
>>> affect (smooth) the surface area maps.
>>>
>>> Is there any solution to also smooth surface area maps with
>>> mris_anatomical_stats?
>>>
>>> I use the Mac FS 5.1.0 version
>>>
>>> Thanks in advance
>>> Best regards
>>> Jürgen Hänggi
>>>
>>>
>>> 
>>> Jürgen Hänggi, Ph.D.
>>> Division Neuropsychology
>>> Institute of Psychology
>>> University of Zurich
>>> Binzmuehlestrasse 14, PO Box 25
>>> 8050 Zurich, Switzerland
>>> 0041 44 635 73 97 (phone office)
>>> 0041 76 445 86 84 (phone mobile)
>>> 0041 44 635 74 09 (fax office)
>>> BIN 4.D.04 (office room number)
>>> j.haenggi[at]psychologie.uzh.ch (email)
>>> http://www.psychologie.uzh.ch/neuropsy/ (website)
>>> http://www.juergenhaenggi.ch (private website)
>>>
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> Division Neuropsychology
> Institute of Psychology
> University of Zurich
> Binzmuehlestrasse 14, PO Box 25
> 8050 Zurich, Switzerland
> 0041 44 635 73 97 (phone office)
> 0041 76 445 86 84 (phone mobile)
> 0041 44 635 74 09 (fax office)
> BIN 4.D.04 (office room number)
> j.haenggi[at]psychologie.uzh.ch (email)
> http://www.psychologie.uzh.ch/neuropsy/ (website)
> http://www.juergenhaenggi.ch (private web

[Freesurfer] Creating DMPFC ROIs in Freesurfer

[Wu, Paula (NIH/NIMH) [F]]

I was wondering whether anyone here has used Freesurfer to create ROIs for the 
Dorsomedial Prefrontal Cortex, or if anyone knows citations of articles that 
have.

Thanks,
Paula

Paula Wu
Postbaccalaureate Intramural Research Training Associate
Section on Functional Imaging Methods
Laboratory of Brain and Cognition
National Institute of Mental Health
(301) 451-9582
w...@mail.nih.gov

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Re: [Freesurfer] MNI to RAS surface coordinates

[Douglas N Greve]

Here are instructions to go from a surface RAS to the mni305 RAS, so 
just invert them.
doug


I have an RAS point on the surface (tkrR tkrA tkrS) ("Vertex RAS" from
tksurfer) and want to compute the MNI305 RAS that corresponds to this
point:

MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]'
   TalXFM: subject/orig/transforms/talairach.xfm
   Norig: mri_info --vox2ras orig.mgz
   Torig: mri_info --vox2ras-tkr orig.mgz

Test: click on a point in tksurfer. Use "Vertex RAS" to compute
MNI305RAS. Compare MNI305RAS to "Vertex MNI Talairach". Also, hit Save
Point in tksurfer. In tkmedit, Goto Saved Point, compare MNI305RAS to
"MNI Coordinates". Note: you may need to use the "Volume RAS" from
tkmedit in the computation above to get an exact match.



On 06/06/2012 09:43 AM, Yolanda Vives wrote:
> Dear Freesurfer experts,
>
> How can I transform from MNI coordinates to RAS surface coordinates?
>
> Regards,
> Yolanda
>
>
> 2012/6/5 Yolanda Vives mailto:yvi...@pic.es>>
>
> Dear Freesurfer experts,
>
> I have performed a VBM analysis with SPM, using some VOIs. Now I
> would like to compare the volumetric results obtained with SPM
> with those of cortical thickness obtained with Freesurfer in the
> same VOIs (approximately).
>
> For this purpose, I would like to transform the MNI coordinates of
> my SPM VOIs into RAS surface coordinates of fsaverage, to draw a
> label of more or less the same size of the SPM VOI and to propage
> it to all the subjects in order to obtain an average cortical
> thickness of this label (VOI) for each subject.
>
> 1) Would this procedure be correct?
>
> 2) How could I transform my MNI coordinates into RAS surface
> coordinates?
>
> Thank you in advance,
> Yolanda
>
>
>
>
> -- 
> Yolanda Vives
> PIC (Port d'Informació Científica)
> Campus UAB, Edificio D
> E-08193 Bellaterra, Barcelona
> Telf. +34 93 586 8232
> http://www.pic.es
> Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html
>
>
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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
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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[Freesurfer] Using an ROI and not correcting/"fixing" the rest of the image

[Kairys, Anson]

Hi,

I am planning on looking at a specific region of interest, and I am wondering 
it is possible to only "quality check" this region and leave the rest of the 
brain as is.

Meaning, can I save the time of going through every slice and re-assigning 
voxels for the entire brain and just focus on making sure the estimation of WM 
etc. is correct in my ROI?

Thanks a lot for any help you can provide.

Best wishes

Anson
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Re: [Freesurfer] Using an ROI and not correcting/"fixing" the rest of the image

[Bruce Fischl]

Hi Anson

yes, that's ok as long as you make sure that the registration 
(sphere.reg) is ok for group results.


cheers
Bruce
On Thu, 7 Jun 2012, Kairys, Anson 
wrote:




Hi,

 

I am planning on looking at a specific region of interest, and I am
wondering it is possible to only ?quality check? this region and leave the
rest of the brain as is.

 

Meaning, can I save the time of going through every slice and re-assigning
voxels for the entire brain and just focus on making sure the estimation of
WM etc. is correct in my ROI?

 

Thanks a lot for any help you can provide.

 

Best wishes

 

Anson

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Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri

[Douglas N Greve]

Hi Leon, I found the problem. mris_make_face_parcellation was actually 
merging several units together. You can get a fixed version from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux
Let me know how it goes
doug

On 06/04/2012 02:44 PM, Leon wrote:
> Hi, Douglas
> I have uploaded the file to the system.
> Also, my new results showed that  when  ic3.tri (instead of ic2.tri) 
> is used as the input, one ROI at the similar location is also missing. 
> Hope it will help you diagnose.
>
> Thanks
> Leon
>
> *From:* Douglas N Greve 
> *To:* Leon 
> *Cc:* FreeSurfer 
> *Sent:* Monday, June 4, 2012 1:00 PM
> *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to 
> transfer ic2.tri
>
> Can you upload the subject to our file drop system?
>
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> 
>
>
>
>
> On 06/04/2012 12:24 PM, Leon wrote:
> > Hi, Douglas
> >
> > Thank you very much for the updated one. I tested the new codes and
> > the problem is still there. The ID for the original version that
> > generates a mask with one missing ROI is:
> >
> > $Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $
> >
> > I remember this is a version I downloaded from a link in FS archive.
> >
> > The ID for the one you sent to me is:
> >
> > $Id: mri_label2vol.c,v 1.34.2.4 2011/09/30 15:19:36 greve Exp $
> >
> > They look almost identical. Do you have any ideas what else may cause
> > this issue and possible workaround?
> >
> > Thank you
> >
> > Leon
> >
> >
> > *From:* Douglas Greve  >
> > *To:* freesurfer@nmr.mgh.harvard.edu 
> 
> > *Sent:* Friday, June 1, 2012 11:29 PM
> > *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to
> > transfer ic2.tri
> >
> >
> > What version are you using? I fix a problem last Sept that might be
> > like this. I've put a new version of mri_label2vol here:
> > 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.linux
> > Try this and let me know if it works.
> > doug
> >
> >
> > On 6/1/12 10:46 PM, Leon wrote:
> >> Hi, Bruce
> >> Here are my two command lines
> >> For transferring the annot from the source template to the target
> >> subject:
> >>
> >> /home/freesurfer/bin/mri_surf2surf --srcsubject ${srcsubject}
> >> --sval-annot rh.ic2.annot --trgsubject ${trgsubject} --trgsurfval
> >> src_2_trg.annot --hemi rh --surfreg sphere.reg0
> >>
> >> Where sphere.reg0 is the registration from the target subject to the
> >> source subject.
> >>
> >> For transfer them to the volume file:
> >>
> >> /home/freesurfer/bin/mri_label2vol --annot src_2_trg.annot --temp
> >> ${fs_dir}/${trgsubject}/mri/brain.mgz --subject ${trgsubject} --hemi
> >> rh --fillthresh 0 --proj frac 0.3 0.8 0.05 --o src_2_trg_annot.mgz
> >> --identity
> >>
> >>
> >> Here is output for one of my transformations:
> >>
> >> Setting mapmethod to nnf
> >> Source registration surface changed to sphere.reg0
> >> Target registration surface changed to sphere.reg0
> >> srcsubject = MacaqueA
> >> srcval= (null)
> >> srctype=
> >> trgsubject = MacaqueB
> >> trgval=
> >> 
> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
> >> trgtype=
> >> srcsurfreg = sphere.reg0
> >> trgsurfreg = sphere.reg0
> >> srchemi= rh
> >> trghemi= rh
> >> frame  = 0
> >> fwhm-in= 0
> >> fwhm-out  = 0
> >> label-src  = (null)
> >> label-trg  = (null)
> >> OKToRevFaceOrder  = 1
> >> Reading source surface reg
> >> /home/freesurfer/freesurfer/subjects/MacaqueA/surf/rh.sphere.reg0
> >> Loading source data
> >> Reading surface file
> >> /home/freesurfer/freesurfer/subjects/MacaqueA/surf/rh.orig
> >> reading colortable from annotation file...
> >> colortable with 162 entries read (originally
> >> /usr/local/freesurfer/lib/bem/ic2.tri)
> >> Reading target surface reg
> >> /home/freesurfer/freesurfer/subjects/MacaqueB/surf/rh.sphere.reg0
> >> Done
> >> Mapping Source Volume onto Source Subject Surface
> >> surf2surf_nnfr: building source hash (res=16).
> >> Surf2Surf: Forward Loop (61916)
> >>
> >> Surf2Surf: Dividing by number of hits (61916)
> >> INFO: nSrcLost = 17467
> >> nTrg121 = 61916, nTrgMulti =0, MnTrgMultiHits = 0
> >> nSrc121 = 35292, nSrcLost = 17467, nSrcMulti = 28910, MnSrcMultiHits
> >> = 0.920927
> >> Saving target data
> >> Converting to target annot
> >> Saving to target annot
> >> 
> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
> >> step2: writing the surface label to volume...
> >> Number of labels: 0
> >> Annot File:
> >> 
> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
> >> Template Volume:
> >> /home/freesurfer/freesurfer/subjects/MacaqueB/mri/brain.mgz
> >> Outut Volume:
> >> 
> /home/freesurfer/freesurfer/subjects/MacaqueB/mri/rh_MacaqueA_to_MacaqueB_fill0_porjs

[Freesurfer] loading surface in freeview

[Kushal Kapse]

hi doug n fellow fs users,

whenever we try to load a fsaverage surface in freeview, it shows me following 
message:

"Surface does not contain valid volume geometry information. It may not align 
with volumes and other surfaces"

this message is limited only to fsaverage surfaces.

was just wondering if this is something to be worried about for further group 
analysis in qdec?.any words on how to fix/avoid this message to reappear???


please let us know


thanks
kk
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[Freesurfer] mri_fill problem

[Shay Ohayon]

Hi,

I am having problem getting mri_fill to run on one of my volumes (it did
work with another monkey, so I assume I am running things right).
I am using v5.0 (but it also happens on 5.1).
The input is a monkey wm file with specified coordinates for the corpus
callosum.
The error I get is: "could not find corpus callosum" (see full log below).
The input volume is available for download here
(
http://tsaolab.caltech.edu/sites/default/files/wm.mgz)

Any takers?  I tried various different coordinates and all of them fail.
A hint may be this statement: "find_cutting_plane:seed point not in
structure! Searching neighborhood..."
which I don't fully understand as the point given is inside a connected
component...

Many thanks,

Shay
Tsao Lab
Caltech




---

reading input volume...done.
searching for cutting planes...INFO: volume does not have linear_transform
set nor lta is given by option.-xform.
INFO: use identity matrix as the talairach transform.
INFO: use src volume parameters for the talairach volume.
voxel to talairach voxel transform
 1.000   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;
find_cutting_plane:seed point not in structure! Searching neighborhood...
Looking for area (min, max) = (350, 1400)
area[0] = 1 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75)
need search nearby
using +/- offset search region where offset is 3.
using +/- offset search region where offset is 6.
using +/- offset search region where offset is 9.
using +/- offset search region where offset is 12.
using +/- offset search region where offset is 15.
using +/- offset search region where offset is 18.
using +/- offset search region where offset is 21.
using +/- offset search region where offset is 24.
using +/- offset search region where offset is 27.
using +/- offset search region where offset is 30.
using +/- offset search region where offset is 33.
using +/- offset search region where offset is 36.
using +/- offset search region where offset is 39.
using +/- offset search region where offset is 42.
using +/- offset search region where offset is 45.
using +/- offset search region where offset is 48.
/space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0/bin/mri_fill:
could not find corpus callosum
/space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0/bin/mri_fill
/space/data/shayo/cooked/test2/mri/wm.nii
/space/data/shayo/cooked/test2/mri/filled.nii -CV 128 117 91: Signal 124
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Re: [Freesurfer] mri_fill problem

[Bruce Fischl]

What's your command line? Are you using voxel coords?



On Jun 7, 2012, at 9:52 PM, Shay Ohayon  wrote:

> Hi,
> 
> I am having problem getting mri_fill to run on one of my volumes (it did work 
> with another monkey, so I assume I am running things right).
> I am using v5.0 (but it also happens on 5.1).
> The input is a monkey wm file with specified coordinates for the corpus 
> callosum.
> The error I get is: "could not find corpus callosum" (see full log below).
> The input volume is available for download here 
> (http://tsaolab.caltech.edu/sites/default/files/wm.mgz)
> 
> Any takers?  I tried various different coordinates and all of them fail.
> A hint may be this statement: "find_cutting_plane:seed point not in 
> structure! Searching neighborhood..."
> which I don't fully understand as the point given is inside a connected 
> component...
> 
> Many thanks,
> 
> Shay
> Tsao Lab
> Caltech
> 
> 
> 
> 
> ---
> 
> reading input volume...done.
> searching for cutting planes...INFO: volume does not have linear_transform 
> set nor lta is given by option.-xform.
> INFO: use identity matrix as the talairach transform.
> INFO: use src volume parameters for the talairach volume.
> voxel to talairach voxel transform
>  1.000   0.000   0.000   0.000;
>  0.000   1.000   0.000   0.000;
>  0.000   0.000   1.000   0.000;
>  0.000   0.000   0.000   1.000;
> find_cutting_plane:seed point not in structure! Searching neighborhood...
> Looking for area (min, max) = (350, 1400)
> area[0] = 1 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75)
> need search nearby
> using +/- offset search region where offset is 3.
> using +/- offset search region where offset is 6.
> using +/- offset search region where offset is 9.
> using +/- offset search region where offset is 12.
> using +/- offset search region where offset is 15.
> using +/- offset search region where offset is 18.
> using +/- offset search region where offset is 21.
> using +/- offset search region where offset is 24.
> using +/- offset search region where offset is 27.
> using +/- offset search region where offset is 30.
> using +/- offset search region where offset is 33.
> using +/- offset search region where offset is 36.
> using +/- offset search region where offset is 39.
> using +/- offset search region where offset is 42.
> using +/- offset search region where offset is 45.
> using +/- offset search region where offset is 48.
> /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0/bin/mri_fill: 
> could not find corpus callosum
> /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0/bin/mri_fill 
> /space/data/shayo/cooked/test2/mri/wm.nii 
> /space/data/shayo/cooked/test2/mri/filled.nii -CV 128 117 91: Signal 124
> 
> 
> 
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Re: [Freesurfer] mri_fill problem

[Shay Ohayon]

Hi Bruce,

Yes. I am using voxel coordinates.

The command line is:
mri_fill /space/data/shayo/cooked/test2/mri/wm.nii
/space/data/shayo/cooked/test2/mri/filled.nii -CV 122 116 91
(I also gave the pons values, but it didn't seem to change anything).

-- Shay
Tsao lab
Caltech


On Thu, Jun 7, 2012 at 6:55 PM, Bruce Fischl wrote:

> What's your command line? Are you using voxel coords?
>
>
>
> On Jun 7, 2012, at 9:52 PM, Shay Ohayon  wrote:
>
> Hi,
>
> I am having problem getting mri_fill to run on one of my volumes (it did
> work with another monkey, so I assume I am running things right).
> I am using v5.0 (but it also happens on 5.1).
> The input is a monkey wm file with specified coordinates for the corpus
> callosum.
> The error I get is: "could not find corpus callosum" (see full log below).
> The input volume is available for download here
> (
> http://tsaolab.caltech.edu/sites/default/files/wm.mgz)
>
> Any takers?  I tried various different coordinates and all of them fail.
> A hint may be this statement: "find_cutting_plane:seed point not in
> structure! Searching neighborhood..."
> which I don't fully understand as the point given is inside a connected
> component...
>
> Many thanks,
>
> Shay
> Tsao Lab
> Caltech
>
>
>
>
> ---
>
> reading input volume...done.
> searching for cutting planes...INFO: volume does not have linear_transform
> set nor lta is given by option.-xform.
> INFO: use identity matrix as the talairach transform.
> INFO: use src volume parameters for the talairach volume.
> voxel to talairach voxel transform
>  1.000   0.000   0.000   0.000;
>  0.000   1.000   0.000   0.000;
>  0.000   0.000   1.000   0.000;
>  0.000   0.000   0.000   1.000;
> find_cutting_plane:seed point not in structure! Searching neighborhood...
> Looking for area (min, max) = (350, 1400)
> area[0] = 1 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75)
> need search nearby
> using +/- offset search region where offset is 3.
> using +/- offset search region where offset is 6.
> using +/- offset search region where offset is 9.
> using +/- offset search region where offset is 12.
> using +/- offset search region where offset is 15.
> using +/- offset search region where offset is 18.
> using +/- offset search region where offset is 21.
> using +/- offset search region where offset is 24.
> using +/- offset search region where offset is 27.
> using +/- offset search region where offset is 30.
> using +/- offset search region where offset is 33.
> using +/- offset search region where offset is 36.
> using +/- offset search region where offset is 39.
> using +/- offset search region where offset is 42.
> using +/- offset search region where offset is 45.
> using +/- offset search region where offset is 48.
> /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0/bin/mri_fill:
> could not find corpus callosum
> /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0/bin/mri_fill
> /space/data/shayo/cooked/test2/mri/wm.nii
> /space/data/shayo/cooked/test2/mri/filled.nii -CV 128 117 91: Signal 124
>
>
>
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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
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> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri

[Leon]

Hi, Douglas


Thank you very much for taking care of it. The ROIs ending with 2 and 5s have 
been correctly labeled and have volumes now after running the fixed version of 
mris_make_face_parcellation.  However, there is still one ROI missing in the 
volume data that is located at the top of the postcentral gyrus after the 
annotation file was transferred from the subject's surface to the volume using 
mri_label2vol. I checked the index of the ROI yesterday (I am at home now and 
do not have access to the data) and I remember the index of the missing ROI is  
vertex_0 and the location of the ROI is identical as the one in the picture I 
attached in the previous email. Do you think it might be because the 
mri_label2vol overlooks the index of 0, as the intensity value in the volumes 
starts with 1? 


I would appreciate your help on this.

Leon



 From: Douglas N Greve 
To: Leon  
Cc: FreeSurfer  
Sent: Thursday, June 7, 2012 2:03 PM
Subject: Re: [Freesurfer] missing ROI when using mri_label2vol to transfer 
ic2.tri
 
Hi Leon, I found the problem. mris_make_face_parcellation was actually 
merging several units together. You can get a fixed version from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux
Let me know how it goes
doug

On 06/04/2012 02:44 PM, Leon wrote:
> Hi, Douglas
> I have uploaded the file to the system.
> Also, my new results showed that  when  ic3.tri (instead of ic2.tri) 
> is used as the input, one ROI at the similar location is also missing. 
> Hope it will help you diagnose.
>
> Thanks
> Leon
>
> *From:* Douglas N Greve 
> *To:* Leon 
> *Cc:* FreeSurfer 
> *Sent:* Monday, June 4, 2012 1:00 PM
> *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to 
> transfer ic2.tri
>
> Can you upload the subject to our file drop system?
>
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> 
>
>
>
>
> On 06/04/2012 12:24 PM, Leon wrote:
> > Hi, Douglas
> >
> > Thank you very much for the updated one. I tested the new codes and
> > the problem is still there. The ID for the
 original version that
> > generates a mask with one missing ROI is:
> >
> > $Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $
> >
> > I remember this is a version I downloaded from a link in FS archive.
> >
> > The ID for the one you sent to me is:
> >
> > $Id: mri_label2vol.c,v 1.34.2.4 2011/09/30 15:19:36 greve Exp $
> >
> > They look almost identical. Do you have any ideas what else may cause
> > this issue and possible workaround?
> >
> > Thank you
> >
> > Leon
> >
> >
> > *From:* Douglas Greve  >
> > *To:* freesurfer@nmr.mgh.harvard.edu 
> 
> > *Sent:* Friday, June 1, 2012 11:29 PM
> > *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to
> > transfer ic2.tri
> >
> >
> > What version are you using? I fix a problem last Sept that might be
> > like this. I've put a new version of mri_label2vol here:
> > 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.linux
> > Try this and let me know if it works.
> > doug
> >
> >
> > On 6/1/12 10:46
 PM, Leon wrote:
> >> Hi, Bruce
> >> Here are my two command lines
> >> For transferring the annot from the source template to the target
> >> subject:
> >>
> >> /home/freesurfer/bin/mri_surf2surf --srcsubject ${srcsubject}
> >> --sval-annot rh.ic2.annot --trgsubject ${trgsubject} --trgsurfval
> >> src_2_trg.annot --hemi rh --surfreg sphere.reg0
> >>
> >> Where sphere.reg0 is the registration from the target subject to the
> >> source subject.
> >>
> >> For transfer them to the volume file:
> >>
> >> /home/freesurfer/bin/mri_label2vol --annot src_2_trg.annot --temp
> >> ${fs_dir}/${trgsubject}/mri/brain.mgz --subject ${trgsubject} --hemi
> >> rh --fillthresh 0 --proj frac 0.3 0.8 0.05 --o src_2_trg_annot.mgz
> >> --identity
>
 >>
> >>
> >> Here is output for one of my transformations:
> >>
> >> Setting mapmethod to nnf
> >> Source registration surface changed to sphere.reg0
> >> Target registration surface changed to sphere.reg0
> >> srcsubject = MacaqueA
> >> srcval    = (null)
> >> srctype    =
> >> trgsubject = MacaqueB
> >> trgval    =
> >> 
> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
> >> trgtype    =
> >> srcsurfreg = sphere.reg0
> >> trgsurfreg = sphere.reg0
> >> srchemi    = rh
> >> trghemi    = rh
> >> frame      = 0
> >> fwhm-in    = 0
> >> fwhm-out  = 0
> >> label-src  =
 (null)
> >> label-trg  = (null)
> >> OKToRevFaceOrder  = 1
> >> Reading source surface reg
> >> /home/freesurfer/freesurfer/subjects/MacaqueA/surf/rh.sphere.reg0
> >> Loading source data
> >> Reading surface file
> >> /home/freesurfer/freesurfer/subjects/MacaqueA/surf/rh.orig
> >> reading colortable from annotation file...
> >> colortable with 162 entries read (originally
> >> /usr/local/free

Re: [Freesurfer] Mris_anatomical_stats: smoothing does not work with surface area maps

[Jürgen Hänggi]

Hi Doug

I correlated a behavioural measure with cortical thickness and surface area
using mri_preroc, mri_surf2surf and mri_glmfit. Now I would like to extract
the individual values of the clusters that correlated with the behavioural
measure. 
Because the individual values should be comparable with the results of the
group, I have to smooth them too.

When using --sval lh.area, the following error occurred:

[Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi%
foreach s ( MOREA_* )
foreach? mri_surf2surf --hemi lh --s $s --sval lh.area --fwhm 15 --tval
lh.area.15.mgh --cortex
foreach? end
ERROR: could not determine type of lh.area
...
...
...
ERROR: could not determine type of lh.area
[Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi%

Thanks
Cheers
Jürgen

On [DATE], "Douglas N Greve" <[ADDRESS]> wrote:

> Use "--sval lh.area". Also, why do you want to smooth it before
> averaging over the ROI?
> doug
> 
> On 06/07/2012 01:29 AM, Jürgen Hänggi wrote:
>> Hi Doug
>> 
>> This is my command line:
>> 
>> mris_anatomical_stats -a area_left_significant_labels.annot -t lh.area
>> -nsmooth 15 -f $s/stats/lh.aparc.a2005s.stats $s lh
>> 
>> In the past, you recommended smoothing the data with mri_surf2surf instead
>> of with mris_anatomical_stats.
>> 
>> For that purpose, I run the following command:
>> 
>> mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval
>> lh.area.15.mgh --cortex
>> 
>> But the following error occurred:
>> 
>> [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi%
>> foreach s ( MOREA_* )
>> foreach? mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval
>> lh.area.15.mgh --cortex
>> foreach? end
>> srcsubject = MOREA_KG002
>> srcval = (null)
>> srctype=
>> trgsubject = MOREA_KG002
>> trgval = lh.area.15.mgh
>> trgtype=
>> srcsurfreg = sphere.reg
>> trgsurfreg = sphere.reg
>> srchemi= lh
>> trghemi= lh
>> frame  = 0
>> fwhm-in= 0
>> fwhm-out   = 15
>> label-src  = (null)
>> label-trg  = lh.cortex.label
>> OKToRevFaceOrder  = 1
>> Reading source surface reg
>> /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.sphere.reg
>> Loading source data
>> Reading surface file
>> /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area
>> nquads=9895939,  nvertices=399
>> ERROR: MRISread: file
>> '/Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area' has many more
>> faces than vertices!
>> Probably trying to use a scalar data file as a surface!
>> 
>> Thanks for help in advance
>> Cheers
>> Jürgen
>> 
>> On [DATE], "Douglas Greve"<[ADDRESS]>  wrote:
>> 
>>> what is your command line?
>>> doug
>>> 
>>> On 6/6/12 5:25 AM, Jürgen Hänggi wrote:
 Dear FS experts
 
 I have done group comparisons wrt thickness and surface area. The
 found clusters were written out as annotations, transformed into each
 individual space, and then the corresponding values were extracted.
 
 When using mris_anatomical_stats, values are different for thickness maps
 depending whether I used the --nsmooth 15 option or not. So good
 so far.
 
 However, when using the same command (see below) for ?h.area files,
 extracted values are the same whether or not I used the --nsmooth option.
 
 It seems that the --nsmooth option in mris_anatomical_stats does not
 affect (smooth) the surface area maps.
 
 Is there any solution to also smooth surface area maps with
 mris_anatomical_stats?
 
 I use the Mac FS 5.1.0 version
 
 Thanks in advance
 Best regards
 Jürgen Hänggi
 
 
 
---
-
 Jürgen Hänggi, Ph.D.
 Division Neuropsychology
 Institute of Psychology
 University of Zurich
 Binzmuehlestrasse 14, PO Box 25
 8050 Zurich, Switzerland
 0041 44 635 73 97 (phone office)
 0041 76 445 86 84 (phone mobile)
 0041 44 635 74 09 (fax office)
 BIN 4.D.04 (office room number)
 j.haenggi[at]psychologie.uzh.ch (email)
 http://www.psychologie.uzh.ch/neuropsy/ (website)
 http://www.juergenhaenggi.ch (private website)
 
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