Re: [Freesurfer] Fwd: comparing lme models
Hi Jorge, My original model is: Intercept + centered age + group + centered age x group + sex; and since I have only two time points I can have only one random factor (as you've stated previously). I have used intercept as the random factor. So, based on your reply, I should fit this model for the covariance: Intercept + centered age + centered age^2 + group + centered age x group + centered age^2 x group + sex; together with three different models for the mean, i.e. intercept, centered age and centered age2 as random factors. When you say different models for the mean, you mean different random factors, right? So I should compare these three random factors with the chi square test to see which random factor to use (i.e., which model for the mean). And then I can test for the significance of centered age, centered age^2, and the two interaction terms to see which fixed factors I can drop from the covariance model? Have I understood you correctly? Thank you! yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway On Wed, Dec 17, 2014 at 5:00 PM, jorge luis jbernal0...@yahoo.es wrote: Hi Lars I'm not sure whether you are talking about comparing different statistical models with the same model for the mean but different models for the covariance or comparing models with different models for the mean itself. In order to use the lreml/chi square test for model comparison you need to have the same model for the mean. In your case it should include: intercept + age + age^2 Then you select which of these variables are going to be treated as random effects based on the appropriate lreml/chi square test. After you select the random effects then you can perform statistical inferences (F-test) to determine whether your age^2 term is significant. If not significant you can drop it from the model. -Jorge -- *De:* Lars M. Rimol lari...@gmail.com *Para:* FS maling list freesurfer@nmr.mgh.harvard.edu; Jorge Luis Bernal Rusiel jbernal0...@yahoo.es *Enviado:* Miércoles 17 de diciembre de 2014 9:42 *Asunto:* [Freesurfer] Fwd: comparing lme models Hi Jorge, I have fitted two lme models that are identical except that one has age and the other has age². When choosing between the models, comparing lreml seems relevant. However, the lreml + chi square test method in FreeSurfer's lme module is meant for comparing full vs. reduced models, so this is not a typical a case for that. Looking at the lreml maps for the two models, I see that in some regions the age model gives a better fit and in other regions the opposite is true. I created difference maps (lreml_age² - lreml_age) and attached figures to illustrate this. In some regions (blue) the model with age yields a higher lreml and in some regions (red) the model with age² yields a higher lreml. Based on this, can I conclude that I might as well use the model with the linear age term? Or should I perform significance tests comparing the lreml maps even if though aren't nested? Thank you! yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) 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] doubt regarding wm.mgz non wm voxels
Hi Elisa if the surfaces are correct (and they seem to have done an impressively good job) then you don't need to. While it worked for this case, I would be a bit concerned that the surfaces won't recover from wm.mgz inaccuracies in others ones though. You might try setting wlo to above the values of the gray matter that it is including (to be passed to mri_segment and mris_make_surfaces using -seg-wlo wlo cheers Bruce On Thu, 18 Dec 2014, elisa veronese wrote: Dear FreeSurfer users, I have a doubt regarding an appearently wrong wm.mgz together with an appearently correct white matter surface. Though the yellow and red lines seem to be correct, should I delete those voxel in the wm.mgz which do not belong to white matter? Thank you. Best, elisa ___ 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] doubt regarding wm.mgz non wm voxels
Thank you. Best, elisa Il 18/dic/2014 16:10 Bruce Fischl fis...@nmr.mgh.harvard.edu ha scritto: Hi Elisa if the surfaces are correct (and they seem to have done an impressively good job) then you don't need to. While it worked for this case, I would be a bit concerned that the surfaces won't recover from wm.mgz inaccuracies in others ones though. You might try setting wlo to above the values of the gray matter that it is including (to be passed to mri_segment and mris_make_surfaces using -seg-wlo wlo cheers Bruce On Thu, 18 Dec 2014, elisa veronese wrote: Dear FreeSurfer users, I have a doubt regarding an appearently wrong wm.mgz together with an appearently correct white matter surface. Though the yellow and red lines seem to be correct, should I delete those voxel in the wm.mgz which do not belong to white matter? Thank you. Best, elisa ___ 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] doubt regarding wm.mgz non wm voxels
Just one additional issue: what am I supposed to do if (please see attached pictures) the wm.mgz file correctly does not include gray matter voxels, but the yellow surface goes into the gray matter? How can I fix this error? Thank you. Best, elisa [image: Immagine in linea 1] [image: Immagine in linea 2] 2014-12-18 16:09 GMT+01:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Elisa if the surfaces are correct (and they seem to have done an impressively good job) then you don't need to. While it worked for this case, I would be a bit concerned that the surfaces won't recover from wm.mgz inaccuracies in others ones though. You might try setting wlo to above the values of the gray matter that it is including (to be passed to mri_segment and mris_make_surfaces using -seg-wlo wlo cheers Bruce On Thu, 18 Dec 2014, elisa veronese wrote: Dear FreeSurfer users, I have a doubt regarding an appearently wrong wm.mgz together with an appearently correct white matter surface. Though the yellow and red lines seem to be correct, should I delete those voxel in the wm.mgz which do not belong to white matter? Thank you. Best, elisa ___ 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. -- elisa ___ 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] longitudinal statistics LGI
HI Jorge,
Thanks for your quick reply. What should we use for the contrast matrix?
the freesurfer LME wiki has:
CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1] zeros(3,5)];
But I wasn't sure if that applies to our analyses. please excuse the naive
questions, we are new to longitudinal LME analyses.
Thanks again
Jon
From: jorge luis jbernal0...@yahoo.es
Sent: Wednesday, December 17, 2014 9:25 AM
To: Freesurfer support list; Jon Alan Wieser
Cc: Krista Lisdahl Medina; alicia.thomas@gmail.com
Subject: Re: [Freesurfer] longitudinal statistics LGI
Hi Jon
We recommend to order the columns of your design matrix in the following way:
First, the intercept term (which is a column of ones); second, the time
covariate; third, any time-varying covariates (eg. cannabis use); fourth, the
group covariates of interest (eg. a binary variable indicating whether the
subject is a patient or control) and their interactions with the time-varying
covariates; finally any other nuisance time-invariant covariate (eg. gender).
So your design matrix is comprised by the following columns:
1. Intercept (a column of ones)
2. Time since baseline
3. cannabis use (time-varying if varies over time for each subject during the
follow-up time)
4. alcohol use (time-varying if varies over time for each subject during the
follow-up time)
5. drug use over time (time-varying if varies over time for each subject during
the follow-up time)
6. gender
7. age at baseline
There is no GUI for setting up the models. Here is an outline of the basic
steps (with only three time points you shouldn't need more than two random
effects):
1-Read your label eg.:
lhcortex = fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label');
2-Read the data file eg.:
[lhY, lhmri] = fs_read_Y('lh.thickness.mgh');
3-Fit a vertex-wise lme model with two random effects for the intercept term
and time eg.:
lhstats1 = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);
4-Fit a vertex-wise lme model with two random effects for the intercept term
and cannabis use eg.:
lhstats2 = lme_mass_fit_vw(X, [1 3], lhY, ni, lhcortex);
And so on with other time-variying covariates...
Now see which model fit produces the best lreml values across vertices in
general and then:
4-Perform vertex-wise inferences using the winner model eg.:
CM.C = [your contrast matrix];
F_lhstats = lme_mass_F(lhstats_winner, CM);
5-Save results eg.:
fs_write_fstats(F_lhstats, lhmri,' sig.mgh', 'sig');
-Jorge
De: Jon Alan Wieser wie...@uwm.edu
Para: jorge luis jbernal0...@yahoo.es; Freesurfer support list
freesurfer@nmr.mgh.harvard.edu
CC: Krista Lisdahl Medina krista.med...@gmail.com;
alicia.thomas@gmail.com alicia.thomas@gmail.com
Enviado: Martes 16 de diciembre de 2014 15:24
Asunto: Re: [Freesurfer] longitudinal statistics LGI
Jorge,
We are interested in examining the impact of cannabis exposure (time-varying
continuous variable) on local gyrification index over 3 time points (baseline,
18 month, 36 month)- so this is a time-varying random effect. I apologize in
advance if these are student questions… we are novices here…
From what you said previously, we would want to model intercept+time, vs
intercept+cannabis use, vs intercept+time+ cannabis use. Vs. intercept+time+
cannabis use.+covariates (alcohol use over time, gender, age, drug use over
time). We are trying to figure out how to do this in Freesurfer/Matlab using
the Wiki (https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels).
There is a great example in there with AD/MCI groups, but none outlining an
example focused on time-varying continuous variables.
So with OUR question, would we organize the data as follows:
Intercept
Time
Cannabis total (changes over time)
Alcohol total (changes over time)
Other Drug total (changes over time)
Gender
Age at baseline
So, a few questions:
1)We need help writing the syntax for Matlab for testing the models
(assuming linear trend was significant):
a. intercept+time, vs
b. intercept+cannabis use, vs
c. intercept+time+ cannabis use. Vs.
d. intercept+time+ cannabis use.+covariates (alcohol use over time, gender,
age, drug use over time)…
i. For example, this is the
linear model for cortical thickness over time for the groups example: Yij = ß1
+ ß2*tij + ß3*t²ij + ß4*sMCIi + ß5*sMCIi*tij + ß6*sMCIi*t²ij + ß7*cMCIi +
ß8*cMCIi*tij + ß9*cMCIi*t²ij + ß10*ADi + ß11*ADi*tij + ß12*ADi*t²ij + ß13*E4i +
ß14*E4i*tij + ß15*Genderi + ß16*BslAgei + ß17*Educationi + b1i + b2i*tij+ eij
ii. This is the design
matrix: [lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,lhcortex,3);
2)Is there a GUI available for setting up these models? (We are assuming
there isn’t and that it is all matlab based.)
3)Once we test these models, is it correct
Re: [Freesurfer] Different significant regions with different cluster wise thresholds
OK, I've figured out what's going on. The cluster @ threshold of 1.3 in superior temporal breaks up into 3 very small clusters when the threshold is changed to 2.0, none of which are significant. There is a cluster in middle temporal at 1.3 but it is not very significant (p=.17), but it stays a single cluster when the threshold is changed to 2.0. The size of the cluster drops by a factor of 2 but it is still large enough to be significant (p=.043). This is just one of the problems with the cluster method. doug On 12/17/2014 05:52 PM, Bronwyn Overs wrote: Hi Doug, The problem is with the int_genderXgroup contrast (between .05 .01 cluster forming thresholds). Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 18/12/2014 4:42 am, Douglas N Greve wrote: There are a bunch of contrasts there. Which one had the discrepancy? doug On 12/15/2014 07:43 PM, Bronwyn Overs wrote: Hi Douglas, I uploaded my glmdir to you on the 3/12/14 (named site-gender-group-prothaplotype.area.lh.glmdir.zip). Can you see what the problem is? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe On 27/11/2014 1:31 pm, Bronwyn Overs wrote: Thanks Douglas, I will upload it then. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe On 27/11/2014 1:30 pm, Douglas Greve wrote: Through the file drop at the end of this email. But you might want to wait until next week as I will be out of the office until Dec 4. doug On 11/26/14 12:50 AM, Bronwyn Overs wrote: Hi Douglas, How exactly should I upload the glmdir? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 11/11/2014 4:19 am, Douglas N Greve wrote: Can you upload the gtlmdir and I'll take a look? On 11/06/2014 08:19 PM, Bronwyn Overs wrote: I believe it is the cluster-forming threshold. I was running the following: mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 1.3 abs --cwpvalthresh 0.05 --2spaces mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 2 abs --cwpvalthresh 0.05 --2spaces Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe On 7/11/2014 4:03 am, Douglas N Greve wrote: Do you mean cluster-wise threshold or cluster-forming threshold? On 11/06/2014 01:12 AM, Bronwyn Overs wrote: Dear Freesurfer Mailing list, While running a glm anlaysis with monte carlo correction (using cluster wise thresholds of .05 .01), I encountered the following issue: When examining the clusters formed for each of the different cluster wise thresholds, the .05 threshold resulted in a superior temporal cluster, while the .01 threshold resulted in a two lateral occipital clusters that did
Re: [Freesurfer] retinotopy in subject volumetric space
What do you mean by the individual's volumetric space? The anatomical space or the functional space? On 12/16/2014 05:18 PM, Benjamin Zimmerman wrote: Thanks for the advice. I thought I would like to use mri_surf2vol, but I am a little confused about the parameters and how they relate to what the retinotopy analysis outputs. To be explicit, I want to view the real.nii.gz and imag.nii.gz files in an individual's volumetric space. I can load these as overlays to the inflated surface using tksurfer subject hemisphere inflated. Then I can configure the overlay to use a color wheel color scale and display as complex to see the retinotopic mapping. I'm not sure how I would go about using mri_surf2vol to recreate this map in volumetric space. Should I just use real.nii.gz and imag.nii.gz as surfval? Where is the registration file outputted in a retinotopy analysis? Thank you for any more help that you can provide, Ben On Mon, Dec 15, 2014 at 3:26 PM, dgw dgwake...@gmail.com mailto:dgwake...@gmail.com wrote: Hi Ben, You should be able to map it back with mri_surf2vol. I haven't done this, but the wiki page looks fairly detailed: http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol HTH D On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com wrote: Hi all, FsFast has an excellent individual retinotopy analysis that allows me to see phase data on the inflated surface of the brain. Is there a way to view the results of the retinotopy analysis in the subject's original volumetric space rather than on the subject's surface space? Thank you for any help, Ben ___ 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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
Re: [Freesurfer] retinotopy in subject volumetric space
I mean the individual's anatomical volumetric space. On Thu, Dec 18, 2014 at 11:53 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: What do you mean by the individual's volumetric space? The anatomical space or the functional space? On 12/16/2014 05:18 PM, Benjamin Zimmerman wrote: Thanks for the advice. I thought I would like to use mri_surf2vol, but I am a little confused about the parameters and how they relate to what the retinotopy analysis outputs. To be explicit, I want to view the real.nii.gz and imag.nii.gz files in an individual's volumetric space. I can load these as overlays to the inflated surface using tksurfer subject hemisphere inflated. Then I can configure the overlay to use a color wheel color scale and display as complex to see the retinotopic mapping. I'm not sure how I would go about using mri_surf2vol to recreate this map in volumetric space. Should I just use real.nii.gz and imag.nii.gz as surfval? Where is the registration file outputted in a retinotopy analysis? Thank you for any more help that you can provide, Ben On Mon, Dec 15, 2014 at 3:26 PM, dgw dgwake...@gmail.com mailto:dgwake...@gmail.com wrote: Hi Ben, You should be able to map it back with mri_surf2vol. I haven't done this, but the wiki page looks fairly detailed: http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol HTH D On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com wrote: Hi all, FsFast has an excellent individual retinotopy analysis that allows me to see phase data on the inflated surface of the brain. Is there a way to view the results of the retinotopy analysis in the subject's original volumetric space rather than on the subject's surface space? Thank you for any help, Ben ___ 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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.
[Freesurfer] surface template N
We are planning to generate a surface template from edited reconstructions of pediatric cortical surfaces (ages 3-11). Any thoughts on the minimum number of subjects should be used to generate the template? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755 ___ 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] surface template N
Hi Jason, I saw this last week. I *think* the original template was on 40 brains, so 40 seems like a good number. In my opinion the bigger issue is the 8 year age range. A 3-year-old's head is much smaller than an 11-year-old's. I'm not sure I would mix them, and if there are enough subjects would suggest binning them into smaller ages. This would be a nice resource regardless, so hopefully this serves as a bump on the subject number question. Anthony On 12/18/14, 2:43 PM, Jason Tourville wrote: We are planning to generate a surface template from edited reconstructions of pediatric cortical surfaces (ages 3-11). Any thoughts on the minimum number of subjects should be used to generate the template? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755 ___ 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. -- Anthony Steven Dick, Ph.D. Assistant Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidique Campus AHC4 454 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: ad...@fiu.edu Webpage: faculty.fiu.edu/~adick ___ 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] From bedpostX and recon-all to tracula
You may have to transpose the bvecs and bvals files. I think that's how Tracula expects them. You can use the attached script to do it. On 12/17/2014 09:18 PM, Katherine Damme wrote: Thanks! That was exactly it! It was a FAT server and so that resolved that issue. Tracula is claiming that the bvecs and bvals don't have the same number of entries. These were the bvecs and bval files created during the trac-all prep process, but when I preprocesed the data previously with FSL the bvecs and bvals that were created did have equal numbers. I tried to specify to use these fsl made bvecs and bvals in the configuration file and it continues to default to the ones that it made. Any ideas? Thank you! Kate On Mon, Dec 15, 2014 at 7:42 PM, Watson, Christopher christopher.wat...@childrens.harvard.edu mailto:christopher.wat...@childrens.harvard.edu wrote: I think certain filesystems don't support sym linking (e.g. FAT32). So that might be it. From: freesurfer-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.da...@gmail.com mailto:katherine.da...@gmail.com] Sent: Monday, December 15, 2014 5:29 PM To: Anastasia Yendiki Cc: Freesurfer support list Subject: Re: [Freesurfer] From bedpostX and recon-all to tracula After removing this I have a new (possibly unrelated error): mv -f /media/Sokol/Subj/041/dmri/bvecs /media/Sokol/Subj/041/dmri/bvecs.norot xfmrot /media/Sokol/Subj/041/dmri/dwi.ecclog /media/Sokol/Subj/041/dmri/bvecs.norot /media/Sokol/Subj/041/dmri/bvecs ln -sf /media/Sokol/Subj/041/dmri/dwi.nii.gz /media/Sokol/Subj/041/dmri/data.nii.gz ln: creating symbolic link `/media/Sokol/Subj/041/dmri/data.nii.gz': Operation not permitted This persists even when I run the command as the root user and regardless of the permissions settings of the folder and the fdwi.nii.gz file. Any ideas? On Mon, Dec 15, 2014 at 3:07 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.harvard.edumailto:ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.harvard.edu wrote: It's hard to tell what's causing the error without seeing the entire trac-all.log. However, by glancing at your config file you seem to still have B0 inhomogeneity correction turned on (dob0 = 1) but without specifying any field map dicoms. I'd turn it off and see if that fixes it. On Mon, 15 Dec 2014, Katherine Damme wrote: Where would I be specifying a directory as an input/output? I used the following cmd: /usr/local/freesurfer/bin/trac-all -prep -c dmri.fy On Sun, Dec 14, 2014 at 7:12 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Katerine the COR-* format is an old one that we don't use anymore. If you specify a directory as an input/output we will assume that it contains COR files, which is probably what you are seeing. cheers Bruce On Sun, 14 Dec 2014, Katherine Damme wrote: At what point is the COR-*.info file made? I got the following error: corRead(): can't open file /media/Sokol/Subj/COR-.info $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/Sokol/Subj/... Linux kate.ad.wcas.northwestern.edu http://kate.ad.wcas.northwestern.eduhttp://kate.ad.wcas.northwestern.edu 2.6.32-431.3.1.el6.x86_64 #1 SMP Fri Dec 13 06:58:20 EST 2013 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fri Dec 12 12:54:40 CST 2014 [ksd770@kate 041]# ls /media/Sokol/Subj/COR-* On Thu, Dec 11, 2014 at 2:48 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.harvard.edumailto:ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.harvard.edu wrote: No, those are field maps used to correct for inhomogeneities in the main magnetic field (which in MRI lingo is referred to as the B0 field, not to be confused with the b=0 images). You can skip that correction (you have to skip it if you don't have field maps). On Thu, 11 Dec 2014, Katherine Damme wrote: I am sorry, I am a bit confused. What am I supposed to be specifying under the b0mlist and b0plist? I thought that it
[Freesurfer] Clarification regarding group specific average template creation
Hello, My question is regarding the registration procedure using a group specific average template. I ran recon-all for my group(with 100 subjects), created an average subject using make_average_subject and then used recon-all qcache by referencing the average template that I just created. I also ran 10,000 iterations of the monte carlo simulation using the above average template for multiple comparisons correction. I plan to use QDEC to analyze my group data. From what I’ve understood so far, during recon-all, each subject is registered to the spherical surface of fsaverage. So, by specifying my average template during the qcache step I’m resampling the data created from the registration with fsaverage onto my own average template. (Is my understanding correct?) I later found this page (https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates ) which outlines a workflow where an average template is created iteratively using the spherical registration parameters of the initial average template. I see that this page was last updated in 2011 and I wanted to know if this still applies to the current version (5.3) If it does apply to the current version, would my workflow be in any way equivalent to the one at the link above? Or would I have to re-register my subjects and re-run all the subsequent steps? I’m quite new to freesurfer and would really appreciate any inputs on this matter. Looking forward to hearing back, -Prad ___ 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] longitudinal statistics LGI
Hi Jorge,
One more newbie question.
what's a good way to visualize the lhstats1.lreml values across the vertices?
Thanks
Jon
From: jorge luis jbernal0...@yahoo.es
Sent: Wednesday, December 17, 2014 9:25 AM
To: Freesurfer support list; Jon Alan Wieser
Cc: Krista Lisdahl Medina; alicia.thomas@gmail.com
Subject: Re: [Freesurfer] longitudinal statistics LGI
Hi Jon
We recommend to order the columns of your design matrix in the following way:
First, the intercept term (which is a column of ones); second, the time
covariate; third, any time-varying covariates (eg. cannabis use); fourth, the
group covariates of interest (eg. a binary variable indicating whether the
subject is a patient or control) and their interactions with the time-varying
covariates; finally any other nuisance time-invariant covariate (eg. gender).
So your design matrix is comprised by the following columns:
1. Intercept (a column of ones)
2. Time since baseline
3. cannabis use (time-varying if varies over time for each subject during the
follow-up time)
4. alcohol use (time-varying if varies over time for each subject during the
follow-up time)
5. drug use over time (time-varying if varies over time for each subject during
the follow-up time)
6. gender
7. age at baseline
There is no GUI for setting up the models. Here is an outline of the basic
steps (with only three time points you shouldn't need more than two random
effects):
1-Read your label eg.:
lhcortex = fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label');
2-Read the data file eg.:
[lhY, lhmri] = fs_read_Y('lh.thickness.mgh');
3-Fit a vertex-wise lme model with two random effects for the intercept term
and time eg.:
lhstats1 = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);
4-Fit a vertex-wise lme model with two random effects for the intercept term
and cannabis use eg.:
lhstats2 = lme_mass_fit_vw(X, [1 3], lhY, ni, lhcortex);
And so on with other time-variying covariates...
Now see which model fit produces the best lreml values across vertices in
general and then:
4-Perform vertex-wise inferences using the winner model eg.:
CM.C = [your contrast matrix];
F_lhstats = lme_mass_F(lhstats_winner, CM);
5-Save results eg.:
fs_write_fstats(F_lhstats, lhmri,' sig.mgh', 'sig');
-Jorge
De: Jon Alan Wieser wie...@uwm.edu
Para: jorge luis jbernal0...@yahoo.es; Freesurfer support list
freesurfer@nmr.mgh.harvard.edu
CC: Krista Lisdahl Medina krista.med...@gmail.com;
alicia.thomas@gmail.com alicia.thomas@gmail.com
Enviado: Martes 16 de diciembre de 2014 15:24
Asunto: Re: [Freesurfer] longitudinal statistics LGI
Jorge,
We are interested in examining the impact of cannabis exposure (time-varying
continuous variable) on local gyrification index over 3 time points (baseline,
18 month, 36 month)- so this is a time-varying random effect. I apologize in
advance if these are student questions… we are novices here…
From what you said previously, we would want to model intercept+time, vs
intercept+cannabis use, vs intercept+time+ cannabis use. Vs. intercept+time+
cannabis use.+covariates (alcohol use over time, gender, age, drug use over
time). We are trying to figure out how to do this in Freesurfer/Matlab using
the Wiki (https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels).
There is a great example in there with AD/MCI groups, but none outlining an
example focused on time-varying continuous variables.
So with OUR question, would we organize the data as follows:
Intercept
Time
Cannabis total (changes over time)
Alcohol total (changes over time)
Other Drug total (changes over time)
Gender
Age at baseline
So, a few questions:
1)We need help writing the syntax for Matlab for testing the models
(assuming linear trend was significant):
a. intercept+time, vs
b. intercept+cannabis use, vs
c. intercept+time+ cannabis use. Vs.
d. intercept+time+ cannabis use.+covariates (alcohol use over time, gender,
age, drug use over time)…
i. For example, this is the
linear model for cortical thickness over time for the groups example: Yij = ß1
+ ß2*tij + ß3*t²ij + ß4*sMCIi + ß5*sMCIi*tij + ß6*sMCIi*t²ij + ß7*cMCIi +
ß8*cMCIi*tij + ß9*cMCIi*t²ij + ß10*ADi + ß11*ADi*tij + ß12*ADi*t²ij + ß13*E4i +
ß14*E4i*tij + ß15*Genderi + ß16*BslAgei + ß17*Educationi + b1i + b2i*tij+ eij
ii. This is the design
matrix: [lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,lhcortex,3);
2)Is there a GUI available for setting up these models? (We are assuming
there isn’t and that it is all matlab based.)
3)Once we test these models, is it correct that we open the spheres
representing the liklihood ratio test results (corrected for multiple
comparisons) and pick the “best” model based on the greatest #/size of
significant clusters?
Jon
Jon Wieser
Re: [Freesurfer] doubt regarding wm.mgz non wm voxels
Hi Elisa try the -seg-wlo I sent you before. Bruce On Thu, 18 Dec 2014, elisa veronese wrote: Just one additional issue: what am I supposed to do if (please see attached pictures) the wm.mgz file correctly does not include gray matter voxels, but the yellow surface goes into the gray matter? How can I fix this error? Thank you. Best, elisa Immagine in linea 1 Immagine in linea 2 2014-12-18 16:09 GMT+01:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Elisa if the surfaces are correct (and they seem to have done an impressively good job) then you don't need to. While it worked for this case, I would be a bit concerned that the surfaces won't recover from wm.mgz inaccuracies in others ones though. You might try setting wlo to above the values of the gray matter that it is including (to be passed to mri_segment and mris_make_surfaces using -seg-wlo wlo cheers Bruce On Thu, 18 Dec 2014, elisa veronese wrote: Dear FreeSurfer users, I have a doubt regarding an appearently wrong wm.mgz together with an appearently correct white matter surface. Though the yellow and red lines seem to be correct, should I delete those voxel in the wm.mgz which do not belong to white matter? Thank you. Best, elisa ___ 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. -- elisa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] surface template N
Hi Jason I would say at least 15, but you can also just check to see when things start to asymptote. I think Christophe found there were diminishing returns after 12 or so, but things have changed somewhat since then, and of course it will depend on the variance on your population. cheers Bruce On Thu, 18 Dec 2014, Jason Tourville wrote: We are planning to generate a surface template from edited reconstructions of pediatric cortical surfaces (ages 3-11). Any thoughts on the minimum number of subjects should be used to generate the template? Thanks, Jason[cleardot.gif] -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755 ___ 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] using mri_convert with multiframe dicom
Hi Doug, Lauren has just reuploaded the multiframe phantoms to your dropbox. Thanks so much for taking a look at this. Jenny Gurney CNDA/Wash U The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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] Clarification regarding group specific average template creation
Hi Prad no, everything is still ni fsaverage space. You would need to run mris_make_template to create a new template, then rerun mris_register cheers Bruce On Thu, 18 Dec 2014, Bharadwaj, Pradyumna - (prad) wrote: Hello, My question is regarding the registration procedure using a group specific average template. I ran recon-all for my group(with 100 subjects), created an average subject using make_average_subject and then used recon-all qcache by referencing the average template that I just created. I also ran 10,000 iterations of the monte carlo simulation using the above average template for multiple comparisons correction. I plan to use QDEC to analyze my group data. From what I’ve understood so far, during recon-all, each subject is registered to the spherical surface of fsaverage. So, by specifying my average template during the qcache step I’m resampling the data created from the registration with fsaverage onto my own average template. (Is my understanding correct?) I later found this page (https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates ) which outlines a workflow where an average template is created iteratively using the spherical registration parameters of the initial average template. I see that this page was last updated in 2011 and I wanted to know if this still applies to the current version (5.3) If it does apply to the current version, would my workflow be in any way equivalent to the one at the link above? Or would I have to re-register my subjects and re-run all the subsequent steps? I’m quite new to freesurfer and would really appreciate any inputs on this matter. Looking forward to hearing back, -Prad ___ 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] Tracula output variability reinit
Hi Peggy - The reinit option is meant to use when you don't have a valid-appearing tract the first time (you have a tract that looks like a single line, which means that the first initialization of the path was poor, i.e., outside the white matter or something like that). If you have a valid-appearing tract with the first initialization, but not with another initialization, then the first one is the one to keep. If you have a case where you have different results but you are unsure which one is valid, I can look at it if you upload here: https://gate.nmr.mgh.harvard.edu/filedrop2/ The nsample is the number of path samples that are saved and added up to give you the final path distribution. In principle, if you found that you were not converging reliably to the same solution with this number of samples (with a valid initialization), you would increase the number. The number of burn-in samples is a number of samples that are run in the very beginning and discarded, before the nsample samples that are actually saved. As long as the algorithm starts from a resonable initial guess, this shouldn't have much of an effect. The nkeep parameter means that 1 sample path is saved for every nkeep sample paths that are drawn. Not keeping every sample increases independence between samples. These are standard aspects of an MCMC algorithm. a.y On Mon, 15 Dec 2014, Peggy Skelly wrote: I've been interested in these 2 questions, since I have similar issues:https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38213.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39282.html What does it mean if I find a valid-appearing tract with reinit=0, but then lose it with reinit=1? How much variability should I expect in the path stats between runs using the same parameters? I haven't gotten as far as the previous question to see if statistical significance changes, but since I'm looking at longitudinal data, I expect the actual white matter changes over time to be rather small. How do the dmrirc parameters nburnin, nsample, and nkeep affect the MCMC process and results? Since the built in randomness should decrease the number of samples is increase, should I just increase nsample? Thanks, Peggy ___ 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] Tracula Question
Hi Emily - One should be a symbolic link to the other, so they should be the exact same file. a.y On Tue, 16 Dec 2014, Emily Louise Belleau wrote: __ Hello, I was wondering what the difference was between the dwi.nii.gz and thd data.nii.gz files. I know based on the website description that the dwi.nii.gz file is the DWI after all corrections have been made but I was unsure about the data.nii.gz file. I am trying a different program that does local tractography and was wondering whether to feed in the dwi.nii.gz or the data.nii.gz files to calculate the diffusion tensors? Thanks, Emily ___ 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] From bedpostX and recon-all to tracula
Hi Kate - The option to use row-formatted (instead of column-formatted) gradient tables was added in a tracula update that came out after freesurfer 5.3 was released. If you want to use this format, you can download the update here: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates You should make sure to download the same build as your 5.3 build, which should be the CentOS 6 64-bit, based on this line that I got from your trac-all.log: build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 a.y On Wed, 17 Dec 2014, Katherine Damme wrote: Thanks! That was exactly it! It was a FAT server and so that resolved that issue. Tracula is claiming that the bvecs and bvals don't have the same number of entries. These were the bvecs and bval files created during the trac-all prep process, but when I preprocesed the data previously with FSL the bvecs and bvals that were created did have equal numbers. I tried to specify to use these fsl made bvecs and bvals in the configuration file and it continues to default to the ones that it made. Any ideas? Thank you! Kate On Mon, Dec 15, 2014 at 7:42 PM, Watson, Christopher christopher.wat...@childrens.harvard.edu wrote: I think certain filesystems don't support sym linking (e.g. FAT32). So that might be it. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.da...@gmail.com] Sent: Monday, December 15, 2014 5:29 PM To: Anastasia Yendiki Cc: Freesurfer support list Subject: Re: [Freesurfer] From bedpostX and recon-all to tracula After removing this I have a new (possibly unrelated error): mv -f /media/Sokol/Subj/041/dmri/bvecs /media/Sokol/Subj/041/dmri/bvecs.norot xfmrot /media/Sokol/Subj/041/dmri/dwi.ecclog /media/Sokol/Subj/041/dmri/bvecs.norot /media/Sokol/Subj/041/dmri/bvecs ln -sf /media/Sokol/Subj/041/dmri/dwi.nii.gz /media/Sokol/Subj/041/dmri/data.nii.gz ln: creating symbolic link `/media/Sokol/Subj/041/dmri/data.nii.gz': Operation not permitted This persists even when I run the command as the root user and regardless of the permissions settings of the folder and the fdwi.nii.gz file. Any ideas? On Mon, Dec 15, 2014 at 3:07 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edumailto:ayend...@nmr.mgh.harvard.edu wrote: It's hard to tell what's causing the error without seeing the entire trac-all.log. However, by glancing at your config file you seem to still have B0 inhomogeneity correction turned on (dob0 = 1) but without specifying any field map dicoms. I'd turn it off and see if that fixes it. On Mon, 15 Dec 2014, Katherine Damme wrote: Where would I be specifying a directory as an input/output? I used the following cmd: /usr/local/freesurfer/bin/trac-all -prep -c dmri.fy On Sun, Dec 14, 2014 at 7:12 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Katerine the COR-* format is an old one that we don't use anymore. If you specify a directory as an input/output we will assume that it contains COR files, which is probably what you are seeing. cheers Bruce On Sun, 14 Dec 2014, Katherine Damme wrote: At what point is the COR-*.info file made? I got the following error: corRead(): can't open file /media/Sokol/Subj/COR-.info $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/Sokol/Subj/... Linux kate.ad.wcas.northwestern.eduhttp://kate.ad.wcas.northwestern.edu 2.6.32-431.3.1.el6.x86_64 #1 SMP Fri Dec 13 06:58:20 EST 2013 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fri Dec 12 12:54:40 CST 2014 [ksd770@kate 041]# ls /media/Sokol/Subj/COR-* On Thu, Dec 11, 2014 at 2:48 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edumailto:ayend...@nmr.mgh.harvard.edu wrote: No, those are field maps used to correct for inhomogeneities in the main magnetic field (which in MRI lingo is referred to as the B0 field, not to be confused with the b=0 images). You can skip that correction (you have to skip it if you don't have field maps). On Thu, 11 Dec 2014, Katherine Damme wrote: I am sorry, I am a bit confused. What am I supposed to be specifying under the b0mlist and b0plist? I thought that it was the B0 low-b image from
Re: [Freesurfer] TRACULA pathway recon failure
Hi Emad - By default, tracula will use aparc+aseg_mask and NOT lowb_brain_mask. So you should make sure aparc+aseg_mask contains the right amount of brain, and then rerun the steps of trac-all that come after the -mask step. a.y On Tue, 16 Dec 2014, Emad Ahmadi wrote: Hi Anastasia, I’ve attached another case in which part of the left frontal pole is removed from the lowb image by FSL BET (opposite of the previous two cases: now lowb is cut too much). As you can see in the last slide, registration of the two masks (aparc+aseg_mask and lowb_brain_mask) are a bit off because of this cut. Can this little offset be the reason of pathways recon failure? Yours, Emad On Dec 16, 2014, at 10:40 AM, Emad Ahmadi e...@nmr.mgh.harvard.edu wrote: Hello Anastasia, I’m reconstructing tracts in a case with subdural hemorrhage, and two pathways are not reconstructed (lh.ccg rh.slft). I found out that the hemorrhage is not included in the structural brain masks, but is included in the diffusion brain masks (please see the attachment). Now I want to remove the hemorrhage from the diffusion brain mask and re-run the pathway recon. Now my question is: which mask(s) in diffusion space should I “shrink” (i.e. remove the hemorrhage), and which steps should I re-run. Thank you so much, Emad Emad Ahmadi, MD --- Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu ___ 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] Tracula: missing or incomplete tracts
Hi - I'm having difficulty with missing or incomplete tracts most of my subjects. I'm hoping for suggestions on where I can look for data problems. The majority of my subjects have at least one missing/incomplete tract, but the specific problematic tract varies across subjects (e.g., one subject has a missing L.Uncinate; another subject has a missing Forceps Major; another is missing the ILF bilaterally, etc.). For my problematic tracts, the path.pd.nii.gz is a single line/curve rather than the diffuse volumetric distribution. I'm not sure how to correct this. I have checked my eigenvectors -- the lines appear to be pointing in the correct directions in my dtifit_V1 -- so I believe my gradient table is correct I've checked my images for motion via visual inspection and by excluding any subjects with dwi_motion outliers in AvgTranslation, AvgRotation, PercentBadSlices, and AvgDropoutScore. I inspected the nodif_brain_mask.nii.gz to look for chunks of missing brain and did not identify any problems here. I've tried increasing the number of control points for each tract. I'd very much appreciate any suggestions on how to troubleshoot next. Thank you, Eileen. ___ 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] Different significant regions with different cluster wise thresholds
Hi Doug, Thanks, that makes it very clear. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 19/12/2014 4:52 am, Douglas N Greve wrote: OK, I've figured out what's going on. The cluster @ threshold of 1.3 in superior temporal breaks up into 3 very small clusters when the threshold is changed to 2.0, none of which are significant. There is a cluster in middle temporal at 1.3 but it is not very significant (p=.17), but it stays a single cluster when the threshold is changed to 2.0. The size of the cluster drops by a factor of 2 but it is still large enough to be significant (p=.043). This is just one of the problems with the cluster method. doug On 12/17/2014 05:52 PM, Bronwyn Overs wrote: Hi Doug, The problem is with the int_genderXgroup contrast (between .05 .01 cluster forming thresholds). Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 18/12/2014 4:42 am, Douglas N Greve wrote: There are a bunch of contrasts there. Which one had the discrepancy? doug On 12/15/2014 07:43 PM, Bronwyn Overs wrote: Hi Douglas, I uploaded my glmdir to you on the 3/12/14 (named site-gender-group-prothaplotype.area.lh.glmdir.zip). Can you see what the problem is? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe On 27/11/2014 1:31 pm, Bronwyn Overs wrote: Thanks Douglas, I will upload it then. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe On 27/11/2014 1:30 pm, Douglas Greve wrote: Through the file drop at the end of this email. But you might want to wait until next week as I will be out of the office until Dec 4. doug On 11/26/14 12:50 AM, Bronwyn Overs wrote: Hi Douglas, How exactly should I upload the glmdir? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 11/11/2014 4:19 am, Douglas N Greve wrote: Can you upload the gtlmdir and I'll take a look? On 11/06/2014 08:19 PM, Bronwyn Overs wrote: I believe it is the cluster-forming threshold. I was running the following: mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 1.3 abs --cwpvalthresh 0.05 --2spaces mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 2 abs --cwpvalthresh 0.05 --2spaces Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe On 7/11/2014 4:03 am, Douglas N Greve wrote: Do
