Re: [Freesurfer] [martinos-tech]
Hi Doug,
Thanks for your reply. I know how to run mri_glmfit-sim. What I'd like to
do is to apply a more liberal threshold to my data to examine the clusters
that fall outside of the MC-corrected threshold. To do this I applied the
mri_surfcluster command with a vertex-wise threshold of p .005, and a
minarea of 50 mm2. My question is how I should interpret the minarea flag.
I want to have some insight in whether this threshold is more liberal than
a threshold of 20 continuous voxels with a p-value of .005 (p .005; k
20) or whether this threshold is more conservative.
Thanks,
Suzanne
On Wed, Sep 11, 2013 at 12:08 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Hi Suzanne, I'll cc the FS list so others can benefit ...
On 09/09/2013 06:02 AM, Suzanne Oosterwijk wrote:
Hi Doug,
I have two follow-up questions to enhance my own understanding of
Freesurfer. I know that MC simulations take into account the smoothness of
the data. I noticed that the smoothing factor of my surface maps is quite
high (around 8/9 fwhm), even though I applied a smoothing factor of 5
during pre-processing. Can you explain to me why the final maps have such a
high fwhm? Is this because of the transformations that are necessary to
create the surfaces?
The final measured FWHM is a composite of the smoothing you applied plus
any smoothness that may already be in the data. Eg, when the surfaces are
created, there is a smoothness constraint that can cause smoothness in the
surfaces. The gyrification index has very high smoothenss. For fMRI, there
is already natural smoothness in the data plus smoothness added due to
interpolation when sampling to the surface.
Another question concerns the relationship between voxels and vertices.
Does one voxel corresponds to one vertex, or is the relationship different?
This may be a very stupid question, but I thoroughly searched the wiki and
the web without finding a straightforward answer.
Vertices and voxels are different entities. A voxel is a 3D box, a vertex
is essentially a 2D triangle on the surface. The surface is made from a
volume, of course. Initially, the square face of a voxel is divided into
two triangles of equal size. The location of the vertices are then adjusted
to get a better fit. Oftentimes, we use the term voxel and vertex
interchangeably because each just represents a data point either on the
surface or in the volume.
The next question is, if I want to apply a liberal threshold to my data
that is similar to say p .005; k 20, then how do I produce this using
the minarea flag in the mri_surfcluster command?
I'm not sure what you mean by p .005. Is that a vertex-wise threshold
(ie, the cluster-forming threshold) or cluster-wise? What is k? If you want
to correct for multiple comparisons, then you can run mri_glmfit-sim. Once
you select a cluster-wise and cluster-forming thresholds (and given the
FWHM and search space), the critical clustersize can be determined.
doug
Thanks in advance for your answers!
Suzanne
On Tue, Sep 3, 2013 at 3:57 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
wrote:
Hi Suzanne, the pre-computed data is for a full hemisphere. if you
have
a smaller search space, then the whole hemi results will be too
conservative. In that case, you should run mri_glmfit-sim without the
--cache and with --sim as indicated in your command line (which looks
correct to me). The simulations can take a while. If you send me your
label, I can compute cached tables for you, so you don't have to keep
running 1 iterations of mri_glmfit-sim
doug
On 09/02/2013 12:04 PM, Suzanne Oosterwijk wrote:
[Attachment(s) #TopText from Suzanne Oosterwijk included below]
Hi all,
I have a question about the Monte Carlo simulation in Freesurfer. I
would like to run a simulation to define the minimum cluster
size in a
specific collection of vertices (say within a ROI label). After
running a masked glmfit the pre-cached simulation doesn’t seem to
correct for the smaller number of vertices; the text files
produce the
same results. I also ran a full simulation to see whether that
made a
difference, and then I got different results. I just want to
make sure
that this is because the smaller volume was applied and not simply
because the “real” simulation can differ from the pre-cached data.
Attached are the different output files, the cached MC with
mask, the
cached MC without mask, the simulation with mask and a normal
cluster
search within the mask (which demonstrates that there are
sub-threshold clusters).
Below is my code,
foreach s (f_fear_c_fear f_disg_c_disg f_mf_c_mf f_notc_c_notc)
pushd ${s}
mri_glmfit --surf fsaverage lh --y
Re: [Freesurfer] TALx coordinates
Hi Doug, just a very naive question about coordinate change: why do we need the fourth component? I mean, shouldn't be the transformation matrix 3x3 instead of 4x4 for a coordinate change in 3D space? thanks! Gari On Wed, Sep 11, 2013 at 12:52 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Yang, I've computed a matrix that should do the trick. If you are in matlab, then M = [0.9975 -0.00730.0176 -0.0429 0.01461.0009 -0.00241.5496 -0.0130 -0.00930.99711.1840 0 0 01.] P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305 Can you give this a shot and see if it makes sense? It will probably be hard to tell since the matrix is pretty close to identity. doug On 09/10/2013 05:17 PM, Yang, Daniel wrote: Thanks, Doug. I am really hoping to get MNI152 (because I also use fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates? Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/10/13 5:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It is an estimate of Tal coords from the MNI305. See http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach If you want MNI305, run mri_surfcluster with --nofixmni doug On 09/10/2013 05:08 PM, Yang, Daniel wrote: Hi all, The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the Talairach system? I find it confusing because mri_surfcluster said: INFO: fixing MNI talairach coordinates Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TALx coordinates
Hi Gari, The transformation actually consists of a 3 x 3 matrix and a 3 x 1 translation vector. The use of a 4 x 4 matrix allows the representation of an affine transformation as a matrix multiplication (http://en.wikipedia.org/wiki/Affine_transformation#Representation). --Thomas On Wed, Sep 11, 2013 at 4:21 PM, Garikoitz Lerma-Usabiaga gariko...@gmail.com wrote: Hi Doug, just a very naive question about coordinate change: why do we need the fourth component? I mean, shouldn't be the transformation matrix 3x3 instead of 4x4 for a coordinate change in 3D space? thanks! Gari On Wed, Sep 11, 2013 at 12:52 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Yang, I've computed a matrix that should do the trick. If you are in matlab, then M = [0.9975 -0.00730.0176 -0.0429 0.01461.0009 -0.00241.5496 -0.0130 -0.00930.99711.1840 0 0 01.] P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305 Can you give this a shot and see if it makes sense? It will probably be hard to tell since the matrix is pretty close to identity. doug On 09/10/2013 05:17 PM, Yang, Daniel wrote: Thanks, Doug. I am really hoping to get MNI152 (because I also use fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates? Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/10/13 5:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It is an estimate of Tal coords from the MNI305. See http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach If you want MNI305, run mri_surfcluster with --nofixmni doug On 09/10/2013 05:08 PM, Yang, Daniel wrote: Hi all, The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the Talairach system? I find it confusing because mri_surfcluster said: INFO: fixing MNI talairach coordinates Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was
[Freesurfer] ASeg Stats is done twice?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi. I try to get information about the progress of my subjects out of the log files, writing a script that reports about the progress and sends progress messages. For that I try to get the individual stages as progress indicator from the recon-all.log. Usually lines like this indicate the start of a stage: #@# ASeg Stats Tue Sep 10 11:12:13 CEST 2013 the date of course is variable and indicates the current date. My problem now is exactly that Stage ASeg Stats, as it occurs twice. the first occurrence is after inflate2 (smooth2, inflate2, aseg stats), the second one is, as documented after cortribbon (parc stats 2, cortical ribbon mask, aseg stats, aparc-to-aseg). But [1] lists only the second occurrence. Is that wanted? is it due to my strategy to run autorecon1, autorecon2 and autorecon3 individually instead of autorecon-all -all? regards and thanks for your help Peter [1] http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlIwONQACgkQi8ffXNvWmYQ5yACgiD/sgP/PR+xsuZJWtGoeFKlL LcYAniH2Q+SSHzPLAc2aTphUyoTm0bv2 =JLDM -END PGP SIGNATURE- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_annotation2annotation?
Hi all, I know I can use mri_label2label and then mris_anatomical_stats -l to obtain the label-based cortical thickness for each individual subject. I also know that there is a tool called mri_annotation2label. But is there a way to convert annotation to each individual subject, so that I can use mris_anatomical_stats -a to obtain the annotation-based cortical thickness for each individual subject? Many thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] FS versions
Dear FS team, I'm using the web portal Neugrid (https://neugrid4you.eu/it) for the analysis of my T1w MRI data with FreeSurfer. In particular, I'm using the *reconall -all*. My question is about possible problems arising from different FS versions. The version provided by Neugrid is the Freesurfer version *5.1.0 *Linux CentOS4 x86_64 When I perform the subsequent manual correction on my workstation, I use Freesurfer version *5.3.0* Linux CentOS4 x86_64 Is this correct? Should I downgrade to the 5.1.0 version also in my workstation? Thank you in advance. Regards, Elisa -- Elisa Veronese - PhD * Research Unit on Brain Imaging and Neuropsychology (RUBIN) * * Inter-University Center for Behavioral Neurosciences (ICBN) University of Udine and University of Verona, Italy ICBN Website: http://icbn.uniud.it/tiki-index.php * ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TALx coordinates
Hi Doug, It's pretty awesome. So accordingly, MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) * 1 MNI152y = (0.0146) MNI305x + (1.0009) MNI305y + (-0.0024) MNI305z + (1.5496) * 1 MNI152z = (-0.0130) MNI305 + (-0.0093) MNI305y + (0.9971) MNI305z + (1.1840) * 1 The last row of the M (i.e., [-0.0429 1.5496 1.1840]') looks like some sort of offset to me, correct? In other words, we are obtaining MNI305 first, Freesurfer convert that to TAL by default (question: is it done linearly or non-linearly?), and then we can manually convert it to MNI152 also. Thanks so much! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/10/13 6:52 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: Hi Yang, I've computed a matrix that should do the trick. If you are in matlab, then M = [0.9975 -0.00730.0176 -0.0429 0.01461.0009 -0.00241.5496 -0.0130 -0.00930.99711.1840 0 0 01.] P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305 Can you give this a shot and see if it makes sense? It will probably be hard to tell since the matrix is pretty close to identity. doug On 09/10/2013 05:17 PM, Yang, Daniel wrote: Thanks, Doug. I am really hoping to get MNI152 (because I also use fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates? Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/10/13 5:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It is an estimate of Tal coords from the MNI305. See http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach If you want MNI305, run mri_surfcluster with --nofixmni doug On 09/10/2013 05:08 PM, Yang, Daniel wrote: Hi all, The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the Talairach system? I find it confusing because mri_surfcluster said: INFO: fixing MNI talairach coordinates Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the
Re: [Freesurfer] [martinos-tech]
Suzanne, p0.005 is the same whether its voxels or vertices. The liberal nature of 20 voxels is vague to begin with as there is two things contributing to how liberal 20 voxels are: (1) voxel size - 20 1mm isotropic voxels is quite different from 20 3mm isotropic voxels; (2) The number of voxels you are testing -- testing 100 voxels and finding 20 that are significant is quite different than testing 10 voxels and finding 20 that are significant. Thus, trying to compare voxels to surface area is quite difficult. I am not sure if there is a way to equate the surface area to voxels given points #1 and #2. It's hard to equate the number of voxels to the surface area because voxels occur outside of the surface as well. You'd have to constrain your analysis to only grey matter and p 0.005 in 20 voxels to be testing the same measurements. Even then, the tests wouldn't quite be the same number or areas. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Wed, Sep 11, 2013 at 4:20 AM, Suzanne Oosterwijk suzanne.oosterw...@gmail.com wrote: Hi Doug, Thanks for your reply. I know how to run mri_glmfit-sim. What I'd like to do is to apply a more liberal threshold to my data to examine the clusters that fall outside of the MC-corrected threshold. To do this I applied the mri_surfcluster command with a vertex-wise threshold of p .005, and a minarea of 50 mm2. My question is how I should interpret the minarea flag. I want to have some insight in whether this threshold is more liberal than a threshold of 20 continuous voxels with a p-value of .005 (p .005; k 20) or whether this threshold is more conservative. Thanks, Suzanne On Wed, Sep 11, 2013 at 12:08 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Suzanne, I'll cc the FS list so others can benefit ... On 09/09/2013 06:02 AM, Suzanne Oosterwijk wrote: Hi Doug, I have two follow-up questions to enhance my own understanding of Freesurfer. I know that MC simulations take into account the smoothness of the data. I noticed that the smoothing factor of my surface maps is quite high (around 8/9 fwhm), even though I applied a smoothing factor of 5 during pre-processing. Can you explain to me why the final maps have such a high fwhm? Is this because of the transformations that are necessary to create the surfaces? The final measured FWHM is a composite of the smoothing you applied plus any smoothness that may already be in the data. Eg, when the surfaces are created, there is a smoothness constraint that can cause smoothness in the surfaces. The gyrification index has very high smoothenss. For fMRI, there is already natural smoothness in the data plus smoothness added due to interpolation when sampling to the surface. Another question concerns the relationship between voxels and vertices. Does one voxel corresponds to one vertex, or is the relationship different? This may be a very stupid question, but I thoroughly searched the wiki and the web without finding a straightforward answer. Vertices and voxels are different entities. A voxel is a 3D box, a vertex is essentially a 2D triangle on the surface. The surface is made from a volume, of course. Initially, the square face of a voxel is divided into two triangles of equal size. The location of the vertices are then adjusted to get a better fit. Oftentimes, we use the term voxel and vertex interchangeably because each just represents a data point either on the surface or in the volume. The next question is, if I want to apply a liberal threshold to my data that is similar to say p .005; k 20, then how do I produce this using the minarea flag in the mri_surfcluster command? I'm not sure what you mean by p .005. Is that a vertex-wise threshold (ie, the cluster-forming threshold) or cluster-wise? What is k? If you want to correct for multiple comparisons, then you can run mri_glmfit-sim. Once you select a cluster-wise and cluster-forming thresholds (and given the
Re: [Freesurfer] mri_tesselate: max vertices 1000000 exceeded
To comment further on this. It appears that - at least in our data - the talairach registration fails frequently (i.e. in more than 60% of the cases) as a result of the larger field inhomogeneities at high field. A good work-around is to use FLIRT for doing the registration. So just use FLIRT to register orig_nu to mni305, and 'translate' the resulting mat file to xfm using tkregister2. Best, Martijn On Mon, Sep 9, 2013 at 3:07 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: glad to hear it Bruce On Mon, 9 Sep 2013, Martijn Steenwijk wrote: Hi Bruce, it seems to work flawlessly. Thanks! On Sat, Sep 7, 2013 at 11:44 AM, Martijn Steenwijk martijnsteenw...@gmail.com wrote: Thanks for your quick reply. It seems that we have some other problems now with the machine, but 'll let you know whether the new mri_tessellate works ;-). On Fri, Sep 6, 2013 at 5:16 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: here you go. Let us know if it works cheers Bruce On Fri, 6 Sep 2013, Martijn Steenwijk wrote: Dear all, I'm trying to process some high res data using the approach Lusebrink proposed, but I'm getting the following error in mri_tessellate: mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ mri_tessellate: max vertices 100 exceeded It seems that max number of faces and vertices is hardly defined in the code. Would it be possible to provide another compiled version (centos6_x86_64-stable-pub-5.**3.0) with these numbers doubled or so? Best regards, Martijn The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] z-scores versus raw_age for correction in GLM_FIT or qdec
Dear Douglas, attached you´ll find the two y.fsgd file from the analysis run in GLM_FIT. the results are completely different (the z-score converted age produces a believable result, while the result correcting with raw age scores seems completely wrong. best regards Olof y.fsgd_raw_age Description: Binary data y.fsgd_zscores Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Could not find .mat
Hi, I am finding a warning at recon-all when creating the folders: INFO: could not find /Path/subject.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 1, coronal unflipped. INFO: if not valid, please provide the information in /Path/subject.mat file What are the consequences of this to image orientation or to registration in further steps? I have sorted the DICOMs using MRIcron (generates .img and .hdr for T1 acquisition). Regards, Pedro. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] rerunning recon-all
I have a somewhat strange question and hopefully someone can help me out. I have a few hundred subjects that have all been run through recon-all, and have gone through some QA. In some of the cases control points have been added or brain masks have been modified etc, and recon-all has been rerun with the 'autorecon2-cp' and autorecon3 flags. My issue now is that my cluster is being upgraded to a different OS, and I'm planning on rerunning on my subjects on the new cluster, but with the same freesurfer version. So my question is how should I go about this. Should a just rerun 'recon-all' from the beginning. If I do this would I be losing the whatever edits I made during the QA procedure? Should I just do rerun with the 'autorecon2-cp' and 'autorecon3'? Am I being overly concerned with a change in computers? Thanks Luke ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Could not find .mat
no, you'll need to figure out which series to give an a file from, but it will figure out the other files in the same series. Also, please cc the list so that others can answer Bruce On Wed, 11 Sep 2013, Pedro Rosa wrote: Hi, Thanks for your help. Is freesurfer able to select T1-w dicoms among dicoms from other acquisitions (dwi, t2w)? I ask this because I have dicoms from all acquisitions in a single folder, and I believe that the process of sorting them may be leading to these problems. Pedro Rosa On 11 Sep 2013, at 03:17 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Pedro you are *far* better off avoiding the analyze format. If you must convert, try nifti, but in general we prefer starting with the dicoms directly. If you give recon-all a *single* image file in the correct (T1-weighted) dicom series we will figure out the other ones cheers Bruce On Wed, 11 Sep 2013, Pedro Rosa wrote: Hi, I am finding a warning at recon-all when creating the folders: INFO: could not find /Path/subject.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 1, coronal unflipped. INFO: if not valid, please provide the information in /Path/subject.mat file What are the consequences of this to image orientation or to registration in further steps? I have sorted the DICOMs using MRIcron (generates .img and .hdr for T1 acquisition). Regards, Pedro. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] t-statistics map using tksurfer
Dear all, Is there a way to visualize vertex wise t-values (t-statistics), instead of p-values, on a vertex map when you are doing group analyses? I successfully generated the p-maps using mri_glfmfit, but I am wondering if vertex-wise maps that represent t-values can be also generated and visualized using tksurfer. Another question I have is that is there a way to generate just average thickness maps within the same group? For example, if want to look at a vertex map that just shows mean thickness of all my controls, how would you generate that file that can be fed into tksurfer? Thanks in advance! Yoon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] reconall question
Hello FreeSurfer experts, I am doing volumetrics study. During the scan we get 2-3 mprage per scan for a subject. While running the FreeSurfer, if I want to use the three mprages for that subject as an input file, may I just keep the three mgz files (001.mgz, 002.mgz and 003.mgz) in the orig folder and run the simple recon all command :Recon-all –s (subject file name) -all or do I need to have some additional flags so that recon all command will use the three T1 images to get one output file? Thanks, Rashmi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Fwd: talairach transforms
-- Forwarded message -- From: swathy p.s swathy.kare...@gmail.com Date: Wed, Sep 11, 2013 at 1:47 AM Subject: talairach transforms To: freesurfer@nmr.mgh.harvard.edu after motiioncor was runned sucessfully,getting error with talairach.comand was as given bellow [root@ml freesurfer]# recon-all -talairach -subjid Stress_v12 Terminal window display was as shown bellow Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r--. 1 root root 346264 Sep 10 23:10 /usr/local/freesurfer/subjects/Stress_v12/scripts/recon-all.log Linux ml 3.3.4-5.fc17.i686 #1 SMP Mon May 7 17:45:26 UTC 2012 i686 i686 i386 GNU/Linux nu_correct: Command not found. # #@# Talairach Tue Sep 10 23:11:50 EDT 2013 /usr/local/freesurfer/subjects/Stress_v12/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux ml 3.3.4-5.fc17.i686 #1 SMP Mon May 7 17:45:26 UTC 2012 i686 i686 i386 GNU/Linux recon-all -s Stress_v12 exited with ERRORS at Tue Sep 10 23:11:55 EDT 2013 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
