Hello there,
I'm trying to resample some thickness difference maps using mri_surf2surf. Unfortunately, I keep getting the following error:
------------------------------------------------------------------- [engram:Multispect] (nmr-std-env) mri_surf2surf --srcsubject 002_MEF_A \ --sval $SUBJECTS_DIR/thickness/002_MEF_A-002_MPRAGE_A/surf/lh.thickness_diff.w \ --src_type curv \ --trgsubject 001_MEF_A \ --tval $SUBJECTS_DIR/thickness/002_MEF_A-002_MPRAGE_A/surf/lh.thickness_diff_resampled_to_001_MEF_A.w \ --trg_type paint \ --hemi lh \ --surfreg sphere.reg
Registration surface changed to sphere.reg srcsubject = 002_MEF_A srcval = /space/engram/1/users/Multispect/thickness/002_MEF_A-002_MPRAGE_A/surf/lh.thickness_diff.w srctype = curv trgsubject = 001_MEF_A trgval = /space/engram/1/users/Multispect/thickness/002_MEF_A-002_MPRAGE_A/surf/lh.thickness_diff_resampled_to_001_MEF_A.w trgtype = paint surfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 Reading source surface reg /space/engram/1/users/Multispect/002_MEF_A/surf/lh.sphere.reg Loading source data Reading curvature file /space/engram/1/users/Multispect/thickness/002_MEF_A-002_MPRAGE_A/surf/lh.thickness_diff.ÔC MRISreadCurvature: could not open /space/engram/1/users/Multispect/thickness/002_MEF_A-002_MPRAGE_A/surf/lh.thickness_diff.ÔC No such file or directory ERROR: reading curvature file -------------------------------------------------------------------
From the initial command output, it appears as though the paths are input correctly, but upon reading the file it appears to be trying to open "lh.thickness_diff.ÔC" instead of "lh.thickness_diff.w" and subsequently failing. Am I doing anything incorrectly here?
Thanks, Julien
The source type is not curv but paint, so use --src_type paint. Even better would be to use mgh, ie, create lh.thickness_diff as an mgh instead of w (ie, lh.thickness_diff.mgh). And then spec the output to be mgh as well. If you use mgh, then there is no need to spec the format. The paint format is being phased out.
doug
Julien wrote:
Hello there,
I'm trying to resample some thickness difference maps using mri_surf2surf. Unfortunately, I keep getting the following error:
[engram:Multispect] (nmr-std-env) mri_surf2surf --srcsubject 002_MEF_A \ --sval $SUBJECTS_DIR/thickness/002_MEF_A-002_MPRAGE_A/surf/lh.thickness_diff.w \ --src_type curv \ --trgsubject 001_MEF_A \ --tval $SUBJECTS_DIR/thickness/002_MEF_A-002_MPRAGE_A/surf/lh.thickness_diff_resampled_to_001_MEF_A.w \ --trg_type paint \ --hemi lh \ --surfreg sphere.reg
Registration surface changed to sphere.reg srcsubject = 002_MEF_A srcval = /space/engram/1/users/Multispect/thickness/002_MEF_A-002_MPRAGE_A/surf/lh.thickness_diff.w
srctype = curv trgsubject = 001_MEF_A trgval = /space/engram/1/users/Multispect/thickness/002_MEF_A-002_MPRAGE_A/surf/lh.thickness_diff_resampled_to_001_MEF_A.w
trgtype = paint surfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 Reading source surface reg /space/engram/1/users/Multispect/002_MEF_A/surf/lh.sphere.reg Loading source data Reading curvature file /space/engram/1/users/Multispect/thickness/002_MEF_A-002_MPRAGE_A/surf/lh.thickness_diff.ÔC
MRISreadCurvature: could not open /space/engram/1/users/Multispect/thickness/002_MEF_A-002_MPRAGE_A/surf/lh.thickness_diff.ÔC
No such file or directory ERROR: reading curvature file
From the initial command output, it appears as though the paths are input correctly, but upon reading the file it appears to be trying to open "lh.thickness_diff.ÔC" instead of "lh.thickness_diff.w" and subsequently failing. Am I doing anything incorrectly here?
Thanks, Julien
Hi, I have two questions: 1. I was wondering if the values of corpus callosum are useful 2. Why the values of the corpus callosum are included in the gray matter data (.aparc.stat)? I need the volume/area of the corpus callosum and I don't understand if the volume given by the stat file is the whole volume of the corpus callosum
Thanks
Valentina
Hi Valentina,
If you are referring to the corpus callosum value from the *h.aparc.annot, this region and the values associated with it are not accurate. Our motivation in including the corpus callosum as a region of interest within our gray matter parcellation atlas was simply as an anatomic placeholder to better delineate the boundaries of the cingulate cortex. As you have mentioned, our anatomic parcellation scheme is for gray matter structures and the corpus callosum is a white matter region and thus intended only as a placeholder, similar to the *h.unknown.label region.
Best regards,
Rahul
---- Rahul S. Desikan rahul@nmr.mgh.harvard.edu
On Thu, 7 Dec 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi, I have two questions:
- I was wondering if the values of corpus callosum are useful
- Why the values of the corpus callosum are included in the gray matter
data (.aparc.stat)? I need the volume/area of the corpus callosum and I don't understand if the volume given by the stat file is the whole volume of the corpus callosum
Thanks
Valentina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, I' compared the regional cortical thickness between two groups of subjects using the statistical parametric maps provided by Freesurfer. I was wondering if there is a way to correct the analysis for the age (the two groups of subjects differ for age) or if the Freesurfer already do that. Thanks Valentina
You can use age as a covariate in a regression (make sure to demean them).
doug
On Fri, 15 Dec 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi, I' compared the regional cortical thickness between two groups of subjects using the statistical parametric maps provided by Freesurfer. I was wondering if there is a way to correct the analysis for the age (the two groups of subjects differ for age) or if the Freesurfer already do that. Thanks Valentina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, I have a question: If I run the same subject twice, without editing, should I aspect to obtain exactly the same results in term of regional and whole cortical thickness or something could change?
Thanks Valentina
I need to compare the regional cortical thickness between two groups of subjects using the statistical parametric maps provided by Freesurfer.
So, I have two classes (patients and healthy volunteers) and one variable (age), if I want correct for age the difference in cortical thickness between these two groups it is enough to write 1, -1, 1 in the contrast vector?
thanks
Valentina
not quite, but almost. There is some randomization that you can disable if you wanted to On Wed, 20 Dec 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi, I have a question: If I run the same subject twice, without editing, should I aspect to obtain exactly the same results in term of regional and whole cortical thickness or something could change?
Thanks Valentina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Could you please quantify "almost"? could you also please explain me how can I eventually disable the randomization?
I have another question that I've already put on the list but the answer never came, maybe is not clear enough: I have two classes (patients and healthy volunteers) and one variable (age), if I want correct for age the difference in cortical thickness between these two groups how can I set the contrast vector?
Thanks Valentina
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, December 20, 2006 4:33 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] variability
not quite, but almost. There is some randomization that you can disable if you wanted to On Wed, 20 Dec 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi, I have a question: If I run the same subject twice, without editing, should I aspect to obtain exactly the same results in term of regional and whole cortical thickness or something could change?
Thanks Valentina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Valentina,
The randomization in the algorithms accounts for about a 0.02% change in thickness results. You can disable randomness (or rather, force seeding the rng with same number) by including the flag -norandomness with recon-all. This flag is available in v3.0.4.
In older versions, do this to disable randomness: create a file called xopts containing this text:
mris_smooth -seed 1234 mris_sphere -seed 1234 mris_fix_topology -seed 1234 mris_ca_label -seed 1234
and then include this flag with recon-all:
-expert xopts
This causes the flag '-seed 1234' to be included with each of the listed binaries, which is what the -norandomness flag would do. If the -expert xopts option is included with each run of the same subject, then the results should be exactly the same (this is how our nightly testing is conducted).
fyi, you can confirm that the flags appear in your runtime commands by including the flag -dontrun with recon-all, which causes recon-all to just printout the commands that it will run.
Nick
On Thu, 2006-12-21 at 10:09 -0500, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Could you please quantify "almost"? could you also please explain me how can I eventually disable the randomization?
I have another question that I've already put on the list but the answer never came, maybe is not clear enough: I have two classes (patients and healthy volunteers) and one variable (age), if I want correct for age the difference in cortical thickness between these two groups how can I set the contrast vector?
Thanks Valentina
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, December 20, 2006 4:33 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] variability
not quite, but almost. There is some randomization that you can disable if you wanted to On Wed, 20 Dec 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi, I have a question: If I run the same subject twice, without editing, should I aspect to obtain exactly the same results in term of regional and whole cortical thickness or something could change?
Thanks Valentina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I have two classes (patients and healthy volunteers) and one variable (age), if I want correct for age the difference in cortical thickness between these two groups it is enough to write 1, -1, 1 in the contrast vector?
thanks
Valentina
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Friday, December 15, 2006 12:08 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] parametric map
You can use age as a covariate in a regression (make sure to demean them).
doug
On Fri, 15 Dec 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi, I' compared the regional cortical thickness between two groups of subjects using the statistical parametric maps provided by Freesurfer.
I
was wondering if there is a way to correct the analysis for the age
(the
two groups of subjects differ for age) or if the Freesurfer already do that. Thanks Valentina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi!
I'm trying to smooth thickness data using mri_surf2surf. The thickness vectors are mapped onto ico7, and I would like to smooth the thickness there (ico7). But when I add the --fwhm option to mri_surf2surf (equivalent to --fwhm-trg), mris_surf2surf looks for a real subject called "ico" (ie $SUBJECTS_DIR/ico/surf/lh.white) instead of the oversampled icosahedron...
This is the type of command I'm using (with freesurfer-Darwin-tiger- stable-pub-v3.0.2, mac os 10.4.8):
mri_surf2surf --hemi lh --srcsubject bert --srcsurfval thickness -- src_type curv --trgsubject ico --trgicoorder 7 --fwhm 30 -- trgsurfval /Users/roberto/Desktop/bertest-lh.mgh --trg_type mgh
without --fwhm everything goes ok, but including it produces at the end an error like this:
(...) MRISread(/freesurfer/subjects/ico/surf/lh.white): could not open file No such file or directory ERROR: could not read /freesurfer/subjects/ico/surf/lh.white
It looks for a subject ico. I think that I could use --fwhm-src to do the smoothing on bert/ lh.white, but then different brain sizes would have different fwhm values after mapped over ico7...
Is there a way of giving an absolute path to the surface used for smoothing? (to /Applications/freesurfer/lib/bem/ic7.tri). Am I doing something wrong?
A last little thing.... how is the number of iterations (à la -- nsmooth) computed from the given fwhm?
thanks in advance! (and have a happy new year :)
roberto
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Using the fwhm option requires a subject because it needs to take into accnt the surface area. ico7 is not a true subject in the freesurfer sense. However, you should have fsaverage in your distribution, and that is the same as ico7.
The conversion from fwhm to niters is here:
gstd = fwhm/sqrt(log(256.0)); //1.14 is a fudge factor based on empirical fit of nearest neighbor niters = floor(1.14*(4*PI*(gstd*gstd))/(7*avgvtxarea) + 0.5);
The avgvtxarea is the average area for the given subject.
doug
On Thu, 4 Jan 2007, Roberto Toro wrote:
Hi!
I'm trying to smooth thickness data using mri_surf2surf. The thickness vectors are mapped onto ico7, and I would like to smooth the thickness there (ico7). But when I add the --fwhm option to mri_surf2surf (equivalent to --fwhm-trg), mris_surf2surf looks for a real subject called "ico" (ie $SUBJECTS_DIR/ico/surf/lh.white) instead of the oversampled icosahedron...
This is the type of command I'm using (with freesurfer-Darwin-tiger- stable-pub-v3.0.2, mac os 10.4.8):
mri_surf2surf --hemi lh --srcsubject bert --srcsurfval thickness --src_type curv --trgsubject ico --trgicoorder 7 --fwhm 30 --trgsurfval /Users/roberto/Desktop/bertest-lh.mgh --trg_type mgh
without --fwhm everything goes ok, but including it produces at the end an error like this:
(...) MRISread(/freesurfer/subjects/ico/surf/lh.white): could not open file No such file or directory ERROR: could not read /freesurfer/subjects/ico/surf/lh.white
It looks for a subject ico. I think that I could use --fwhm-src to do the smoothing on bert/lh.white, but then different brain sizes would have different fwhm values after mapped over ico7...
Is there a way of giving an absolute path to the surface used for smoothing? (to /Applications/freesurfer/lib/bem/ic7.tri). Am I doing something wrong?
A last little thing.... how is the number of iterations (à la --nsmooth) computed from the given fwhm?
thanks in advance! (and have a happy new year :)
roberto
This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu