Re: [Freesurfer] smoothing functional data on smoothwm surface
Dear Doug, unfortunately, I don't know how to define the source (EPI) and target (smoothwm) within the mri_surf2surf command to apply smoothing on the FEAT functional data. My aim is to apply smoothing of the FEAT functional data AFTER being resampled to the smoothwm (to avoid deficient smoothing due to attached cortical banks given by VBR-approaches) mri_surf2surf --s PM_02173 --hemi lh --sval ??? --fwhm 10 --trgsurfval smoothwm is smooth-out a better option? --smooth-out (to apply smoothing after resampling to the smoothwm) ps: Might tksurfer be an alternative? Using: tksurfer subject lh smoothwm -overlay [FEAT functional] -overlay-reg [...anat2exf.register.dat ] and apply smoothing by using Tools-- Surface -- Overlay Smoothing? Kindly regards, Christopher Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve Gesendet: Montag, 16. Juni 2014 17:30 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] smoothing functional data on smoothwm surface Use mri_surf2surf with the --fwhm option doug On 6/16/14 3:13 PM, Milde, Christopher wrote: Dear Freesurfers, I'm interested in smoothing preprocessed (but unsmoothed) functional FEAT data, which was coregistered and resampled to the anatomical surface (using: reg-feat2anat/feat2surf). I want to apply smoothing on the functional data preferentially on a surface which doesn't suffer from metric distortions (like the inflated OR sphere). I thought about using the smoothwm surface. Questions: Which command can I use for smoothing the feat functional data on the smoothwm AND furthermore, how can I extract the cluster maxima afterwards??? I'm thankful for any helpful comment, Greetz, Christopher ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] smoothing functional data on smoothwm surface
Did you look at the documentation by running it with --help? The sval is the result of mri_vol2surf. Don't use the smoothwm. It will automatically use the white surface to compute the fwhm which is what you want. On 6/18/14 11:09 AM, Milde, Christopher wrote: Dear Doug, unfortunately, I don't know how to define the source (EPI) and target (smoothwm) within the mri_surf2surf command to apply smoothing on the FEAT functional data. My aim is to apply smoothing of the FEAT functional data AFTER being resampled to the smoothwm (to avoid deficient smoothing due to attached cortical banks given by VBR-approaches) mri_surf2surf --s PM_02173 --hemi lh --sval ??? --fwhm 10 --trgsurfval smoothwm is smooth-out a better option? --smooth-out (to apply smoothing after resampling to the smoothwm) ps: Might tksurfer be an alternative? Using: tksurfer subject lh smoothwm --overlay [FEAT functional] -overlay-reg [...anat2exf.register.dat ] and apply smoothing by using ToolsàSurface àOverlay Smoothing? Kindly regards, Christopher *Von:*freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *Im Auftrag von *Douglas Greve *Gesendet:* Montag, 16. Juni 2014 17:30 *An:* freesurfer@nmr.mgh.harvard.edu *Betreff:* Re: [Freesurfer] smoothing functional data on smoothwm surface Use mri_surf2surf with the --fwhm option doug On 6/16/14 3:13 PM, Milde, Christopher wrote: Dear Freesurfers, I'm interested in smoothing preprocessed (but unsmoothed) functional FEAT data, which was coregistered and resampled to the anatomical surface (using: reg-feat2anat/feat2surf). I want to apply smoothing on the functional data preferentially on a surface which doesn't suffer from metric distortions (like the inflated OR sphere). I thought about using the smoothwm surface. *Questions:* Which command can I use for smoothing the feat functional data on the smoothwm AND furthermore, how can I extract the cluster maxima afterwards??? I'm thankful for any helpful comment, Greetz, Christopher ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 ___ 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] Researcher/Postdoctoral position: Multimodal Neuroimaging, Twins, Autism and ADHD, Karolinska Institutet
Dear list, One Researcher/postdoc position is available in our group at Karolinska Institutet in Stockholm. Application Deadline is June the 30th 2014. --- Group and Project --- Karolinska Institutet Center of Neurodevelopmental Disorders (KIND) http://ki.se/kind KIND is an excellence center for research, development, education and clinical practice in the area of developmental psychopathology. The Roots of Autism and ADHD Twin Study Sweden (RATSS) is a frontline research project within KIND, focusing on monozygotic twins discordant for autism spectrum disorder and other neurodevelopmental disorders. For the first time ever, twins are examined on multiple levels: behavior, cognition, neurobiology, environment, and genetics to elucidate the etiology of neuropsychiatric disorders. Functional and structural neuroimaging using MRI are an integral part of RATSS. Scanning is performed at the Karolinska Institutet MR Research Center, using a 3 Tesla MR scanner (GE MR750). To date, 80 pairs have been examined. --- Position --- As a neuroimaging researcher (typically, but not necessarily post-doc) in RATSS, while working in a team of scientists, you are mainly responsible for the acquisition and analyses of the multimodal brain imaging data. Diffusion Tensor Imaging (DTI), resting state functional MRI and structural T1 analyses will be integrated into hierarchical network models such as brain connectome. We expect motivation, routine and professionalism in administrative tasks, grant application and article writing. This work will be done in close collaboration with other partners (e.g. Dr. Peter Fransson, the Dept. of Clinical Neuroscience (KI); Institute Pasteur (Paris), EUAIMS project, Mt Sinai (New York)). All details about the position can be found here: https://ki.mynetworkglobal.com/se/what:job/jobID:37590/where:4/ Applications should be submitted here: https://ki.mynetworkglobal.com/en/what:login/jobID:37590/where:4/ Please note that we DO NOT ACCEPT applications being submitted by email. To be considered, your application must be submitted through the application system. Best regards, Elodie Cauvet for KIND Élodie CAUVET | PhD Karolinska Institutet Center of Neurodevelopmental Disorders (KIND) Gävlegatan 22B, floor 8 | 113 30 Stockholm +46 (0)8 51452706 | +46 (0)728 774 058 elodiemailto:elodie.cau...@ki.se.cau...@ki.semailto:elodie.cau...@ki.se | ki.se/kindhttp://ki.se/ki/jsp/polopoly.jsp;jsessionid=aMdk8ad4iRL6OYOdFn?l=end=130 ___ Karolinska Institutet – a medical university ___ 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: Improving translation of Choi striatal ROIs to original domain
Hi Freesurfers,
My processing stream involves moving the parcellated functional networks of
Yeo and Choi to original subject domain to do connectivity analyses. While
my process works very well for the Yeo networks I'm rather unsatisfied by
the results of the Choi translations.
I'm hoping someone has some suggestions for improving things so that the
Choi ROIs map onto individual subjects nearly as well as the general
Freesurfer striatal segmentations.
NB - I work with AD patients, so I'm sure part of the problem is
atrophy-based. However, I'm sure there are ways to improve things...
*My current pipeline involves two steps:*
*mri_vol2vol \*
*--mov Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz \*
*--targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader \*
*--o FSL_choi_17Net_MNI152_tight_parcellation.nii.gz --no-save-reg --interp
nearest*
*mri_label2vol \*
*--seg FSL_choi_17Net_MNI152_tight_parcellation.nii.gz \*
*--reg $SUBJECTS_DIR/{$subj}/mri/transforms/reg.mni152.2mm.dat \*
*--invertmtx \*
*--o Choi_17Network_tight_striatum_orig.nii.gz \*
*--temp $SUBJECTS_DIR/{$subj}/mri/orig.mgz*
I suspect one way to improve things would be to do a recon-all based
procedure, but I have no clue what commands within the recon-all domain
that would involve.
Thanks for your suggestions.
--
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
___
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Fwd: Improving translation of Choi striatal ROIs to original domain
Hi Paul
Thomas Yeo (ccd) would be the best person to help you, but he may not be
reading email for a while
cheers
Bruce
On Wed, 18 Jun 2014, Paul Beach wrote:
Hi Freesurfers,
My processing stream involves moving the parcellated functional networks of
Yeo and Choi to original subject domain to do connectivity analyses. While
my process works very well for the Yeo networks I'm rather unsatisfied by
the results of the Choi translations.
I'm hoping someone has some suggestions for improving things so that the
Choi ROIs map onto individual subjects nearly as well as the general
Freesurfer striatal segmentations.
NB - I work with AD patients, so I'm sure part of the problem is
atrophy-based. However, I'm sure there are ways to improve things...
My current pipeline involves two steps:
mri_vol2vol \
--mov Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz \
--targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader \
--o FSL_choi_17Net_MNI152_tight_parcellation.nii.gz --no-save-reg --interp
nearest
mri_label2vol \
--seg FSL_choi_17Net_MNI152_tight_parcellation.nii.gz \
--reg $SUBJECTS_DIR/{$subj}/mri/transforms/reg.mni152.2mm.dat \
--invertmtx \
--o Choi_17Network_tight_striatum_orig.nii.gz \
--temp $SUBJECTS_DIR/{$subj}/mri/orig.mgz
I suspect one way to improve things would be to do a recon-all based
procedure, but I have no clue what commands within the recon-all domain that
would involve.
Thanks for your suggestions.
--
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program - MSU Cognitive and Geriatric Neurology Team (CoGeNT)
___
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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] Linear Mixed Models in FS?
Hi Jorge, Thank you for your reply! Again considering the same model from before intercept(random effect) + centered age + group + group x centered age + sex I think what is confusing me is that I think of the [centered age] covariate as a column vector which will contain the centered age of both the control- and the case group. This is how it would be seen in a GLM using the same design matrix. Therefore it is difficult for me to understand how the contrast [0 1 0 0 0] can inform us about the control group alone. To me it would seem obvious that this contrast tells me something about the effect of [centered age] on the whole of the sample, regardless of the group each subject belongs to. On the other hand, I agree with you that the interaction term could tell us something about the effect of [centered age] on the case-group by considering the contrast vector [0 0 0 1 0]. Just for the sake of argument, please consider the following model intercept(random effect) + (1-group) x centered age + group + group x centered age + sex and compare to the one presented above. Here (1-group) is a column vector which is 1 where the [group] vector is 0, and vice versa. This difference ensures that the second term only includes numbers from the control-group. Applying the contrast [0 1 0 0 0] to this model, would this not be more appropriate for consider the effect of [centered age] on the control-group alone? Given your previous answers I suspect I'm missing something here, but I would greatly appreciate if you could please take the time to explain to me how I've gone wrong. Thanks! LMR --- Hi LMR 1) Yes, you should use n-1 (0/1) covariates to model n groups. Eg. (Controls, Case 1 and Case 2) the model would be: intercept(random effect) + centered age?(might be a random effect too)?+ ?Case1 + Case1 x centered age + Case2 + Case2 x centered age + sex 2)In model: intercept(random effect) + centered age + group + group x centered age + sex the fourth coefficient is the interaction term that represents the difference in slope between the patient and control groups. This is easy to see from your Question 1 equations. It's also easy to see from those equations that [0 1 0 0 0] tests the effect of time in the control group since the group-specific slope is only equal to the coefficient of the time covariate (the second covariate) when the group covariate is zero (i.e for the controls). Hope this makes sense. Best -Jorge -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ 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] label from volume on decimated surface
Hello Freesurfer experts, I want to project a label from a volume on a decimated surface. Normally I do something like this to generate a label from the volume: mri_vol2surf --src subjects/foobar/mri/aparc+aseg.mgz --regheader foobar --hemi lh --surf pial --out test.mgh mri_cor2label --i test.mgh --id 1024 --surf foobar lh pial --l test.label Unfortunately this does not work if I decimated the lh.pial surface before (for example using mris_decimate). Do you have a suggestion how to accomplish this? Kai ___ 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] problem of Label file
Hi Wang what is the overlay? That is what must be giving the crazy values Bruce On Wed, 18 Jun 2014, kangchengwang0...@gmail.com wrote: Dear Bruce, Thank you very much for your response. The area which I made label could be seen in the figure (below). Is the reason for large number that the line was outside the blue area? [IMAGE] Wang Kangcheng ___ 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] Linear Mixed Models in FS?
Hi LMR If the interaction term is not statistically significant then there is no evidence of the existence of two different groups in your sample (as far as the longitudinal trajectory is concerned they are all controls, the groups might be different at baseline though). This is why main effects are only tested after the interactions have been previously tested. In your model a common “base time slope” is assumed for both groups (the second coefficient) but you are also explicitly modeling the possibility of the case-group slope being exceeding the control/common base slope by an extra quantity. That quantity is the interaction term. Hope this makes sense Best -Jorge De: Lars M. Rimol lari...@gmail.com Para: FS maling list freesurfer@nmr.mgh.harvard.edu Enviado: Miércoles 18 de junio de 2014 8:57 Asunto: Re: [Freesurfer] Linear Mixed Models in FS? Hi Jorge, Thank you for your reply! Again considering the same model from before intercept(random effect) + centered age + group + group x centered age + sex I think what is confusing me is that I think of the [centered age] covariate as a column vector which will contain the centered age of both the control- and the case group. This is how it would be seen in a GLM using the same design matrix. Therefore it is difficult for me to understand how the contrast [0 1 0 0 0] can inform us about the control group alone. To me it would seem obvious that this contrast tells me something about the effect of [centered age] on the whole of the sample, regardless of the group each subject belongs to. On the other hand, I agree with you that the interaction term could tell us something about the effect of [centered age] on the case-group by considering the contrast vector [0 0 0 1 0]. Just for the sake of argument, please consider the following model intercept(random effect) + (1-group) x centered age + group + group x centered age + sex and compare to the one presented above. Here (1-group) is a column vector which is 1 where the [group] vector is 0, and vice versa. This difference ensures that the second term only includes numbers from the control-group. Applying the contrast [0 1 0 0 0] to this model, would this not be more appropriate for consider the effect of [centered age] on the control-group alone? Given your previous answers I suspect I'm missing something here, but I would greatly appreciate if you could please take the time to explain to me how I've gone wrong. Thanks! LMR --- Hi LMR 1) Yes, you should use n-1 (0/1) covariates to model n groups. Eg. (Controls, Case 1 and Case 2) the model would be: intercept(random effect) + centered age?(might be a random effect too)?+ ?Case1 + Case1 x centered age + Case2 + Case2 x centered age + sex 2)In model: intercept(random effect) + centered age + group + group x centered age + sex the fourth coefficient is the interaction term that represents the difference in slope between the patient and control groups. This is easy to see from your Question 1 equations. It's also easy to see from those equations that [0 1 0 0 0] tests the effect of time in the control group since the group-specific slope is only equal to the coefficient of the time covariate (the second covariate) when the group covariate is zero (i.e for the controls). Hope this makes sense. Best -Jorge -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ 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 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] Fwd: Improving translation of Choi striatal ROIs to original domain
Hi Bruce,
Thanks for the response.
I actually got this pipeline partly from Thomas a few months back. However,
I wasn't sure if anyone had suggestions perhaps for a recon-all based
command for going from the MNI152 1mm template-based fit to individual
subjects. The recon-all/Freesurfer inherent striatal parcellations are so
well fitted to even my severe AD patients, so I was hoping I could somehow
adapt this to the Choi ROIs.
On Wed, Jun 18, 2014 at 8:45 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Paul
Thomas Yeo (ccd) would be the best person to help you, but he may not be
reading email for a while
cheers
Bruce
On Wed, 18 Jun 2014, Paul Beach wrote:
Hi Freesurfers,
My processing stream involves moving the parcellated functional networks
of
Yeo and Choi to original subject domain to do connectivity analyses. While
my process works very well for the Yeo networks I'm rather unsatisfied by
the results of the Choi translations.
I'm hoping someone has some suggestions for improving things so that the
Choi ROIs map onto individual subjects nearly as well as the general
Freesurfer striatal segmentations.
NB - I work with AD patients, so I'm sure part of the problem is
atrophy-based. However, I'm sure there are ways to improve things...
My current pipeline involves two steps:
mri_vol2vol \
--mov Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
\
--targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader \
--o FSL_choi_17Net_MNI152_tight_parcellation.nii.gz --no-save-reg
--interp
nearest
mri_label2vol \
--seg FSL_choi_17Net_MNI152_tight_parcellation.nii.gz \
--reg $SUBJECTS_DIR/{$subj}/mri/transforms/reg.mni152.2mm.dat \
--invertmtx \
--o Choi_17Network_tight_striatum_orig.nii.gz \
--temp $SUBJECTS_DIR/{$subj}/mri/orig.mgz
I suspect one way to improve things would be to do a recon-all based
procedure, but I have no clue what commands within the recon-all domain
that
would involve.
Thanks for your suggestions.
--
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program - MSU Cognitive and Geriatric Neurology Team
(CoGeNT)
___
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.
--
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
___
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] Fwd: Improving translation of Choi striatal ROIs to original domain
Hi,
The recon-all based striatal parcellations are based on the anatomy of each particular subject, guided by a probabilistic atlas. That is inherently likely to be more accurate that just taking a set of ROIs/parcellations defined in some (non-probabilistic)
atlas and warping them to each subject via an affine transformation, which is what it sounds like you are doing with the Choi ROIs.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Tel: 314-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: Paul Beach pabea...@gmail.com
Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Date: Wednesday, June 18, 2014 8:52 AM
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Cc: Thomas Yeo thomas@nus.edu.sg, Yeo, Boon Thye Thomas -- Boon Thye Thomas Yeo ytho...@csail.mit.edu
Subject: Re: [Freesurfer] Fwd: Improving translation of Choi striatal ROIs to original domain
Hi Bruce,
Thanks for the response.
I actually got this pipeline partly from Thomas a few months back. However, I wasn't sure if anyone had suggestions perhaps for a recon-all based command for going from the MNI152 1mm template-based fit to individual subjects. The recon-all/Freesurfer
inherent striatal parcellations are so well fitted to even my severe AD patients, so I was hoping I could somehow adapt this to the Choi ROIs.
On Wed, Jun 18, 2014 at 8:45 AM, Bruce Fischl
fis...@nmr.mgh.harvard.edu wrote:
Hi Paul
Thomas Yeo (ccd) would be the best person to help you, but he may not be reading email for a while
cheers
Bruce
On Wed, 18 Jun 2014, Paul Beach wrote:
Hi Freesurfers,
My processing stream involves moving the parcellated functional networks of
Yeo and Choi to original subject domain to do connectivity analyses. While
my process works very well for the Yeo networks I'm rather unsatisfied by
the results of the Choi translations.
I'm hoping someone has some suggestions for improving things so that the
Choi ROIs map onto individual subjects nearly as well as the general
Freesurfer striatal segmentations.
NB - I work with AD patients, so I'm sure part of the problem is
atrophy-based. However, I'm sure there are ways to improve things...
My current pipeline involves two steps:
mri_vol2vol \
--mov Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz \
--targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader \
--o FSL_choi_17Net_MNI152_tight_parcellation.nii.gz --no-save-reg --interp
nearest
mri_label2vol \
--seg FSL_choi_17Net_MNI152_tight_parcellation.nii.gz \
--reg $SUBJECTS_DIR/{$subj}/mri/transforms/reg.mni152.2mm.dat \
--invertmtx \
--o Choi_17Network_tight_striatum_orig.nii.gz \
--temp $SUBJECTS_DIR/{$subj}/mri/orig.mgz
I suspect one way to improve things would be to do a recon-all based
procedure, but I have no clue what commands within the recon-all domain that
would involve.
Thanks for your suggestions.
--
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program- MSUCognitive andGeriatricNeurologyTeam (CoGeNT)
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- College of Osteopathic Medicine
- Neuroscience Program
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Re: [Freesurfer] problem of Label file
Dear Bruce, The overlay was sig.mgh,which was the result of thickness between patient and control. The line must be within the area of blue, right? Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0...@gmail.com / wangkangcheng@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China ___ 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] FreeSurfur Installation problems
It certainly does seem like their are permissions issue. From your message below, the 'rm' and 'mv' command complained about inadequate permissions... and the recon-all.env command failed as well. You've installed freesurfer on your Desktop folder, which is somewhat out of the ordinary, though not a problem in itself. Make sure you have adequate permissions to that folder. And get the recon-all command that you issued working (recon-all -s bert -autorecon1). Once that works the GUIs should work as well. -Zeke On 06/17/2014 05:36 PM, Jonathan Thomas O'Neil wrote: Hello, I am having issue with running Tkmedit, tksurfer, qdec, and recon-all. Based on the error messages I am receiving, it appears that the program think I have permission issues. I have checked these and that does not appear to be the case. Here are the errors I am getting. Please let me know what I can do *tkmedit: *mss169:Desktop jto929$ tkmedit bert orig.mgz === ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu : : Now exiting... * * *tksurfer: for tksurfer it seems to run, but then stops. a view appears on the screen, but then immediately disappears. * * * s169:Desktop jto929$ tksurfer bert rh pial subject is bert hemiis rh surface is pial surfer: current subjects dir: /Users/jto929/Desktop/freesurfer/subjects surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/jto929/Desktop checking for nofix files in 'pial' Reading image info (/Users/jto929/Desktop/freesurfer/subjects/bert) Reading /Users/jto929/Desktop/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Users/jto929/Desktop/freesurfer/subjects/bert/mri/orig.mgz surfer: vertices=133299, faces=266594 surfer: single buffered window surfer: tkoInitWindow(bert) mss169:Desktop jto929$ *qdec: *mss169:Desktop jto929$ qdec Segmentation fault recon-all mss169:Desktop jto929$ recon-all -s bert -autorecon1 INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/jto929/Desktop/freesurfer/subjects Actual FREESURFER_HOME /Users/jto929/Desktop/freesurfer rm: /Users/jto929/Desktop/freesurfer/subjects/bert/scripts/recon-all.cmd: Permission denied mv: rename /Users/jto929/Desktop/freesurfer/subjects/bert/scripts/recon-all.env to /Users/jto929/Desktop/freesurfer/subjects/bert/scripts/recon-all.env.bak: Permission denied /Users/jto929/Desktop/freesurfer/subjects/bert/scripts/recon-all.env: Permission denied. /Users/jto929/Desktop/freesurfer/subjects/bert/scripts/recon-all.env: Permission denied. ___ 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.
[Freesurfer] Mouse use for tkmedit
Hi, I'm using freesurfer on a mac computer, and therefore my mouse doesn't have a right click or middle button. Is there an alternative way to make edits in tkmedit (such as to correct voxels erroneously classified as white matter in recon-all) without using the mouse buttons? Thanks, Caroline ___ 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] GLM: What's the link?
Hello Freesurfers, I can not tell what the link is from the Mathematical Background in mri_glmfit . Also, why is GLM performed instead of a linear regression (OLS or weighted LS )? I can not see how logistic, probit, etc is better. Thank you very much! Sincerely, Ye ___ 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] Can not visualize read_surf.m output with matlab
Dear Freesurfers,
I tried the following in matlab
[coords,faces] =read_surf('\subject\surf\rh.orig')
Hp = patch('vertices',coords,'faces',faces(:,[1 3 2]),...
'facecolor',[.5 .5 .5],'edgecolor','none')
camlight('headlight','infinite')
vertnormals = get(Hp,'vertexnormals');
Matlab returns the following error:
Error using patch
Faces values must be = 1.0
Indeed, there are 0's in faces. Is this a mistake?
Thank you very much!
Sincerely,
Ye
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[Freesurfer] Segfault error
Hello, I am running into a segfault error when trying to use tkmedit or tksufer. I am currently running OSX 10.7.5 and have the most current version of XQuartz installed. Below are the contents of the .xdebug files: .xdebug_tkmedit: tkmedit started: Wed Jun 18 10:58:41 2014 /Applications/freesurfer/tktools/tkmedit.bin bert brainmask.mgz $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /Users/jaceking Set subject home dir to /Applications/freesurfer/subjects/bert Using interface file /Applications/freesurfer/tktools/tkmedit.tcl Segfault Setting global interpreter xDebug stack (length: 2) 01: main() 01: Setting global interpreter 00: 00: .xdebug_tksurfer: Segfault Initializing glut xDebug stack (length: 1) 00: 00: Initializing glut Segfault Initializing glut I also get a Segmentation fault note when trying to launch qdec. Do you have suggestions on how to fix this? Thanks in advance for your assistance. Best, Jace King ___ 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] GLM: what does mris_preproc do?
Hello Freesurfers, Is there a way that I can take a look at the content of the output of mris_preproc? Thank you very much! Sincerely, Ye On Sun, Apr 6, 2014 at 5:33 PM, ye tian tianye...@gmail.com wrote: Dear Doug, Thank you very much! Sincerely, Ye On Sun, Apr 6, 2014 at 5:32 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: It resamples them to a common space (the average subject) but does not average them together. The result is a stack which is a single file with multiple subject it in it ready for GLM analysis doug On 4/6/14 6:18 PM, ye tian wrote: Dear Doug, Thank you, but I am only more confused after reading the summary. The summary basically reaffirms my understanding that mris_preproc gives an average subject. How can this be an appropriate data for GLM, which for sure needs multiple data points? Thank you! Sincerely, Ye On Sun, Apr 6, 2014 at 5:12 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Hi Ye, have you looked at the mris_preproc help? You can access it with mris_preproc --help. Let me know if that does not answer your questions doug On 4/6/14 6:09 PM, ye tian wrote: Hello Freesurfers, I understand that the output of mris_preproc can be the input of mris_glmfit. In mris_glmfit, a GLM is performed. Does mris_preproc give you a smoothed average of all the subjects? If that's the case, how can you perform a GLM with just the average? Don't you need the data (smoothed or not) of all subjects? Thank you very much! Sincerely, Ye ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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. ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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. ___ 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] GLM: What's the link?
In this case, GLM stands for General Linear Model, and not Generalized Linear Model (although the former is a subset of the latter). See e.g. http://en.wikipedia.org/wiki/Generalized_linear_model#Confusion_with_general_linear_models From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of ye tian [tianye...@gmail.com] Sent: Wednesday, June 18, 2014 12:46 PM To: Freesurfer Subject: [Freesurfer] GLM: What's the link? Hello Freesurfers, I can not tell what the link is from the Mathematical Background in mri_glmfit . Also, why is GLM performed instead of a linear regression (OLS or weighted LS )? I can not see how logistic, probit, etc is better. Thank you very much! Sincerely, Ye ___ 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] GLM: what does mris_preproc do?
It is just a script so you can view it with any text editor doug On 6/18/14 7:15 PM, ye tian wrote: Hello Freesurfers, Is there a way that I can take a look at the content of the output of mris_preproc? Thank you very much! Sincerely, Ye On Sun, Apr 6, 2014 at 5:33 PM, ye tian tianye...@gmail.com mailto:tianye...@gmail.com wrote: Dear Doug, Thank you very much! Sincerely, Ye On Sun, Apr 6, 2014 at 5:32 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It resamples them to a common space (the average subject) but does not average them together. The result is a stack which is a single file with multiple subject it in it ready for GLM analysis doug On 4/6/14 6:18 PM, ye tian wrote: Dear Doug, Thank you, but I am only more confused after reading the summary. The summary basically reaffirms my understanding that mris_preproc gives an average subject. How can this be an appropriate data for GLM, which for sure needs multiple data points? Thank you! Sincerely, Ye On Sun, Apr 6, 2014 at 5:12 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Ye, have you looked at the mris_preproc help? You can access it with mris_preproc --help. Let me know if that does not answer your questions doug On 4/6/14 6:09 PM, ye tian wrote: Hello Freesurfers, I understand that the output of mris_preproc can be the input of mris_glmfit. In mris_glmfit, a GLM is performed. Does mris_preproc give you a smoothed average of all the subjects? If that's the case, how can you perform a GLM with just the average? Don't you need the data (smoothed or not) of all subjects? Thank you very much! Sincerely, Ye ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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. ___ 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] GLM: What's the link?
Dear Watson, Thank you very much! Sincerely, Ye On Wed, Jun 18, 2014 at 12:36 PM, Watson, Christopher christopher.wat...@childrens.harvard.edu wrote: In this case, GLM stands for General Linear Model, and not Generalized Linear Model (although the former is a subset of the latter). See e.g. http://en.wikipedia.org/wiki/Generalized_linear_model#Confusion_with_general_linear_models From: freesurfer-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of ye tian [ tianye...@gmail.com] Sent: Wednesday, June 18, 2014 12:46 PM To: Freesurfer Subject: [Freesurfer] GLM: What's the link? Hello Freesurfers, I can not tell what the link is from the Mathematical Background in mri_glmfit . Also, why is GLM performed instead of a linear regression (OLS or weighted LS )? I can not see how logistic, probit, etc is better. Thank you very much! Sincerely, Ye ___ 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 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] GLM: what does mris_preproc do?
Dear Doug, These files typically end with .mgh. I tired opening them with text editors and them typically give a file of unreadable characters like: @駺9窣,@!礱@ ^@$圚@萗@.?@6%@.溋@*鳣!址@+?@!编@3岰@ 祺@€錊7]@@E褸%N(?錹?諕驚]Z@?蔮@0MU@'灔@+緌@2Pq@ %?@7?@*y7@ @,?y@ Sincerely, Ye On Wed, Jun 18, 2014 at 12:40 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: It is just a script so you can view it with any text editor doug On 6/18/14 7:15 PM, ye tian wrote: Hello Freesurfers, Is there a way that I can take a look at the content of the output of mris_preproc? Thank you very much! Sincerely, Ye On Sun, Apr 6, 2014 at 5:33 PM, ye tian tianye...@gmail.com wrote: Dear Doug, Thank you very much! Sincerely, Ye On Sun, Apr 6, 2014 at 5:32 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: It resamples them to a common space (the average subject) but does not average them together. The result is a stack which is a single file with multiple subject it in it ready for GLM analysis doug On 4/6/14 6:18 PM, ye tian wrote: Dear Doug, Thank you, but I am only more confused after reading the summary. The summary basically reaffirms my understanding that mris_preproc gives an average subject. How can this be an appropriate data for GLM, which for sure needs multiple data points? Thank you! Sincerely, Ye On Sun, Apr 6, 2014 at 5:12 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Hi Ye, have you looked at the mris_preproc help? You can access it with mris_preproc --help. Let me know if that does not answer your questions doug On 4/6/14 6:09 PM, ye tian wrote: Hello Freesurfers, I understand that the output of mris_preproc can be the input of mris_glmfit. In mris_glmfit, a GLM is performed. Does mris_preproc give you a smoothed average of all the subjects? If that's the case, how can you perform a GLM with just the average? Don't you need the data (smoothed or not) of all subjects? Thank you very much! Sincerely, Ye ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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. ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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. ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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. ___ 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] Mouse use for tkmedit
Hi Caroline, On Jun 18, 2014, at 18:08 , Caroline Lewis carolineemmale...@gmail.com wrote: Hi, I'm using freesurfer on a mac computer, and therefore my mouse doesn't have a right click or middle button. Is there an alternative way to make edits in tkmedit (such as to correct voxels erroneously classified as white matter in recon-all) without using the mouse buttons? Are you using apple's X11 or XQuartz? Then start any X application (like tkmedit bert T1.mgz from a terminal with the freesurfer environment sourced); select the X11 item in the application bar (on top of the screen); select Preferences…: select the Input tab; check the Emulate three button mouse. Now holding the option key while clicking emulates the middle button, holding the command key emulates the right button. In case you need simultaneous presses of more than one button, go buy a real three button mouse ;). Hope that helps… Sebastian Thanks, Caroline ___ 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
Re: [Freesurfer] problem of Label file
no, not necessarily. The blue area is just the suprathreshold region. Are the numbers reported in the overlay reasonable? You can email us the sig.mgh and we'll take a look if you want (email us the label also) On Wed, 18 Jun 2014, wangkangcheng_gmail wrote: Dear Bruce, The overlay was sig.mgh,which was the result of thickness between patient and control. The line must be within the area of blue, right? Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0...@gmail.com / wangkangcheng@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China ___ 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] V1 and V2 labels valid with clinical populations?
Does anyone know of any support (i.e. articles/data) suggesting that the V1 and V2 labels automatically created in the Freesurfer pipeline, especially when looking at surface area/gyrification, are valid to use with clinical populations? In particular, visually deprived populations? Thanks! Krista ___ 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] V1 and V2 labels valid with clinical populations?
Hi Krista I don't think we have any idea. The labels are based purely on anatomy, but whether those areas keep their functional specification we have no idea. let us know if you find out though! Bruce On Wed, 18 Jun 2014, krista kelly wrote: Does anyone know of any support (i.e. articles/data) suggesting that the V1 and V2 labels automatically created in the Freesurfer pipeline, especially when looking at surface area/gyrification, are valid to use with clinical populations? In particular, visually deprived populations? Thanks! Krista ___ 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] V1 and V2 labels valid with clinical populations?
OK thanks. I see a lot of pubs using these labels. Can anyone provide any advice on how to justify using these labels in clinical populations without also collecting functional retinotopy data? On Wed, Jun 18, 2014 at 4:13 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Krista I don't think we have any idea. The labels are based purely on anatomy, but whether those areas keep their functional specification we have no idea. let us know if you find out though! Bruce On Wed, 18 Jun 2014, krista kelly wrote: Does anyone know of any support (i.e. articles/data) suggesting that the V1 and V2 labels automatically created in the Freesurfer pipeline, especially when looking at surface area/gyrification, are valid to use with clinical populations? In particular, visually deprived populations? Thanks! Krista ___ 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 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] Segfault error
Hello, Can you please email me the contents of your /Application/freesurfer/build-stamp.txt file? And also what version of OSX you are running by typing sw_vers (without quotes) on the command line? -Zeke On 06/18/2014 01:02 PM, Jace Bradford King wrote: Hello, I am running into a segfault error when trying to use tkmedit or tksufer. I am currently running OSX 10.7.5 and have the most current version of XQuartz installed. Below are the contents of the .xdebug files: .xdebug_tkmedit: tkmedit started: Wed Jun 18 10:58:41 2014 /Applications/freesurfer/tktools/tkmedit.bin bert brainmask.mgz $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /Users/jaceking Set subject home dir to /Applications/freesurfer/subjects/bert Using interface file /Applications/freesurfer/tktools/tkmedit.tcl Segfault Setting global interpreter xDebug stack (length: 2) 01: main() 01: Setting global interpreter 00: 00: .xdebug_tksurfer: Segfault Initializing glut xDebug stack (length: 1) 00: 00: Initializing glut Segfault Initializing glut I also get a Segmentation fault note when trying to launch qdec. Do you have suggestions on how to fix this? Thanks in advance for your assistance. Best, Jace King ___ 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] GLM: what does mris_preproc do?
oh, sorry, I thought you wanted to look at the script itself. The .mgh files are binary files with pixel data. You can view them with tksurfer/freeview. You can load them with MRIread.m in matlab On 6/18/14 8:41 PM, ye tian wrote: Dear Doug, These files typically end with .mgh. I tired opening them with text editors and them typically give a file of unreadable characters like: @?9?,@!?@ ^@$?@?@.?@6%@.?@*?!?@+?@!?@3?@ ?@EUR?7]@?@E?%N(?????]Z@??@0MU@'?@+?@2Pq@%?@7?@*y7@ ?@,?y@ Sincerely, Ye On Wed, Jun 18, 2014 at 12:40 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It is just a script so you can view it with any text editor doug On 6/18/14 7:15 PM, ye tian wrote: Hello Freesurfers, Is there a way that I can take a look at the content of the output of mris_preproc? Thank you very much! Sincerely, Ye On Sun, Apr 6, 2014 at 5:33 PM, ye tian tianye...@gmail.com mailto:tianye...@gmail.com wrote: Dear Doug, Thank you very much! Sincerely, Ye On Sun, Apr 6, 2014 at 5:32 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It resamples them to a common space (the average subject) but does not average them together. The result is a stack which is a single file with multiple subject it in it ready for GLM analysis doug On 4/6/14 6:18 PM, ye tian wrote: Dear Doug, Thank you, but I am only more confused after reading the summary. The summary basically reaffirms my understanding that mris_preproc gives an average subject. How can this be an appropriate data for GLM, which for sure needs multiple data points? Thank you! Sincerely, Ye On Sun, Apr 6, 2014 at 5:12 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Ye, have you looked at the mris_preproc help? You can access it with mris_preproc --help. Let me know if that does not answer your questions doug On 4/6/14 6:09 PM, ye tian wrote: Hello Freesurfers, I understand that the output of mris_preproc can be the input of mris_glmfit. In mris_glmfit, a GLM is performed. Does mris_preproc give you a smoothed average of all the subjects? If that's the case, how can you perform a GLM with just the average? Don't you need the data (smoothed or not) of all subjects? Thank you very much! Sincerely, Ye ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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
Re: [Freesurfer] Can not visualize read_surf.m output with matlab
Our indices are zero based, and matlab is one based. That is probably the
problem
Bruce
On Jun 18, 2014, at 1:09 PM, ye tian tianye...@gmail.com wrote:
Dear Freesurfers,
I tried the following in matlab
[coords,faces] =read_surf('\subject\surf\rh.orig')
Hp = patch('vertices',coords,'faces',faces(:,[1 3 2]),...
'facecolor',[.5 .5 .5],'edgecolor','none')
camlight('headlight','infinite')
vertnormals = get(Hp,'vertexnormals');
Matlab returns the following error:
Error using patch
Faces values must be = 1.0
Indeed, there are 0's in faces. Is this a mistake?
Thank you very much!
Sincerely,
Ye
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