[Freesurfer] contrast matrix
Dear Prof Donald McLaren
I am sorry to disturb you! I have four discrete variables {factor 1(A,B),
factor 2(C,D), factor 3(G,H), and gender(M,F)} and a continuous variable (age),
I want to use the GLM to analysis the result of the interaction among factor
1(A,B), factor 2(C,D) and factor 3(E,F) regressing out the effect of gender and
age, and I have 16 classes: MACG,MACH, MADG, MADH, MBCG, MBCH, MBDG, MBDH,
FACG,FACH, FADG, FADH, FBCG, FBCH, FBDG, FBDH, so I design the contrast is
following:
1 -1 -1 1 -1 1 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 1 -1 -1 1 -1 1 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
is correct? thank you very much!
look forward for your reply!
Bo Xiang
At 2012-11-21 04:07:37,MCLAREN, Donald mclaren.don...@gmail.com wrote:
On Tue, Nov 20, 2012 at 12:56 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
Thanks Donald. Is this the standard way to do this? I had used 8 rows
instead of 4 with the difference being that 8 rows gives you an opportunity
to look for an effect in males OR females.
Yes. Having 8 rows would tell you if you have an interaction between
factor 1 and 2 in either males or females. My 4 rows only tell you if
the interaction exists. Technically speaking, one would run the
three-way interaction first. If nothing existed then you do the
two-way interaction as I suggested. If there is a three-way
interaction, then you would use Doug's approach of the interaction in
either males or females.
If there is an effect in both
males and females but the effects go in opposite directions, then the 4 row
implementation will resolve to 0 (no effect). Or am I misunderstanding
something (again:)?
Nope. You are right. If the male and female effects are different,
then they could cancel each other out. If you suspect this to be the
case, then you should be able to demonstrate a three-way interaction.
thanks!
doug
On 11/20/2012 01:50 PM, MCLAREN, Donald wrote:
Bo,
Doug asked me to chime in on your issue. Here are some points that you
(and others) will hopefully find useful.
(1) Inferences are two-step process. First, you create and estimate
the design matrix. Every column in the design matrix accounts can
account for some of the variance in the data. Second, you have
contrasts that allow you to infer specific effects. Because the model
contains your covariates, you are always controlling for the
covariates and by extension any factor/covariate not in the contrast.
(2) Forming contrasts is often the most difficult thing to do. I
assume that your three factors (1, 2, and gender) are all
between-subject factors. If one of them is a within-subject factor
please let me know and disregard the rest of the email. The final
F-contrast will have 4 rows (factor 1 levels-1)*(factor 2 levels
-1)=(3-1)*(3-1)=2*2=4
The following is an outline for creating contrasts:
(a) Start simple - difference between levels of 1 factor
(b) Define your null hypothesis: AO=AP=AQ
(c) Make it equal to 0: AO-AP=0 AND AP-AQ=0
(d) Repeat for the other levels of the factor...
BO-BP=0 AND BP-BQ=0
CO-CP=0 AND CP-CQ=0
(e) Now combine them AO-AP=BO-BP=CO-CP AND AP-AQ=BP-BQ=CP-CQ
(f) Make them equal to 0:
AO-AP-BO+BP=0
BO-BP-CO+CP=0
AP-AQ-BP+BQ=0
BP-BQ-CP+CQ=0
(g) Expand them to include gender, for example:
AO-AP-BO+BP=0 becomes FAO-FAP-FBO+FBP+MAO-MAP-MBO+MBP=0
Since the contrast now has 2 columns per level, you should divide all
values by 2. This will produce the correct amplitude and statistics.
If you leave the values as 1 and -1, then you will have an incorrect
amplitude, but the statistics will still be correct.
(h) Fill in the respective columns of your design matrix.
(3) The degrees of freedom are defined based on the rows of the
F-matrix and the number of rows in the design matrix. The F-test has a
numerator and denominator degrees of freedom. F(n,d).
Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital
and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Tue, Nov
Re: [Freesurfer] surf2vol
Doug The .nii.gz file is completely empty and doesn't come up on any viewer (fslview, tkmedit, freeview, mricron etc). The .gi files I've generated appear to be tracking in probtrackx (though slowly on my laptop - probably not expected given the sizes of the surfaces). I can also generate binary volumetric masks from the labels using mri_binarize (though they are a little bit speckled - with scattered blank voxels). On my installation I'm having some intermittent difficulties with tkmedit and tksurfer (not consistently opening, sometimes coming up with bus error). Freeview is opening consistently though. I'm not sure if this could be having an affect but I was planning on reinstalling freesurfer today to see if that fixed it. Thank you again for your help Dan Does leftfrontallobe.nii.gz overlay properly in tkmedit? eg, tkmedit subject orig.mgz -surfs -overlay leftfrontallobe.nii.gz -fminmax .5 1 dougOn 03/26/2013 07:20 AM, Daniel Lumsden wrote: Bruce Many thanks - that's given me a lot more guidance. Following the help, i've put together the command below: mri_surf2vol --hemi lh --template path to/orig.mgz --outvol path to where I want the file/leftfrontallobe.nii.gz --surfval path to/left_frontal_lobe.gii --fillribbon --volregidentity mov07 Where mov07 is my subjid and left_frontal_lobe.gii is the surface I've generated from the label files to run in probtrakx. This command runs, but produces and empty nifti file. I've changed the output to .mgz with similar effect. I've substituted the rawavg.mgz file for the orig.mgz file, and tried both .nii.gz and .mgz versions of both files and still get an empty output file. The subject is in my $SUBJECTS_DIR. Is there a way to check the .gii files? I generated them using label2surf, having used mris_convert to convert the lh.white and rh.white files from the surf folder for my subject to lh.white.asc and rh.white.asc. Thank you again for your help. Dan Date: Mon, 25 Mar 2013 14:59:28 -0400 From: fis...@nmr.mgh.harvard.edu To: doclums...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surf2vol Hi Dan try using mri_surf2vol instead (it has a much bigger help, thanks to Doug0 Bruce On Mon, 25 Mar 2013, Daniel Lumsden wrote: Dear All Apologies for what I'm sure is a very basic question. I'm new to using freesurfer, and would like to generate cortical parcellations for running in probtrakx. I have followed the instructions from various sources and have managed to generate the parcellations from recon-all, extract the label files from the parcellation, then use mri_mergelabels and label2surf to generate the the .gii files needed for probtrakx. I'd like to be able to display the surface files for illustrative purposes, but I'm struggling to apply the surf2vol command. From the terminal window I can see that the commands required are: surf2vol surf refvol outvol convention I presume that surf is the .gii file I'm trying to visualise, and outvol is to specify the name of the output volume the command will generate, but what should I be using as the refvol? I would be very grateful for any guidance. Please accept my apologies if I've missed a very obvious online explanation for this and thank you in advance. Dan Lumsden Clinical Research Fellow 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 -- 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: 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
[Freesurfer] Fwd: Cortical thickness in average space
Thanks Bruce for your answer, as you asked I'm forwarding this question to the list in case any other can answer this. We already have the surface generated by mri_preproc, now we are trying to read it using the matlab function read_mgh. It returns a 4-D matrix, how can we interpret this data to get the cortical thickness values at each vertex of every subject? Rafa Gabi 2013/3/26 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Rafa and Gabi yes, that's pretty much what the -qcache flag does in recon-all. Or you can use mri_surf2surf to do it. cheers Bruce On Tue, 26 Mar 2013, Rafa X wrote: Hi Freesurfers, We would need to obtain the cortical thickness of each subject in the space of the average subject (built from our subject population), Does it exists? If so, Can I use the label files produced by mri_surfcluster to directly extract the mean cortical thickness of each ROI in each subject? We want to avoid to trasform each cluster to every subject. Thank you all in advance, Rafa Gabi. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Correlation with cortical thickness
Dear all, I've a question regarding computing correlations with cortical thicknesses on the surface; Suppose I have two variables for each subject: (age and weight) and I want to compute the correlation between cortical thickness and weight, corrected for age. Option 1: Fsgd contains: Variables weight Contrast file contains: 0 1 Option 2: Fsgd contains: Variables age weight Contrast file contains: 0 0 1 Is it true that the effect of age is regressed out in the second option; and it computes the correlation between CT and weight after correcting for age? Best, Martijn ___ 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] Question regarding the subject directory
Hi folks! I would like to use a different subject dirctory (setenv SUBJECTS_DIR full path to subject dir). Does freesurfer still finds the folders which are located in the default subjects directory of the FS installation? Or are they simply not needed for the recon-all process ? I refer to cvs_avg35 etc. not to the test data sets. Please excuse if this question is stupid ... but considering the processsing time ... Many thanks in advance, Luke___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] iSurf BrainView now available for Windows 8 {Disarmed}
Today Microsoft approved iSurf BrainView version for Windows 8 Tablets and computers. It's a free App. http://apps.microsoft.com/windows/en-us/app/brainview/be2623f5-c5e3-4295-a28e-d3f64dc19266 BrainView is a Brain MRI tutor based on the MRI automatic segmentation produced by FreeSurfer. FreeSurfer is a software package developed by investigators at the Athinoula A. Martinos Center for Biomedical Imaging. This App uses its automatic segmentation to produce an automatic atlas of neuroimaging based on T1 MRI Images. It also displays 3D accurate models of brain cortex with automatic structure labeling. A great tool for teaching brain MRI and for learning neuroanatomy. For more reference on the educational use of iSurf BrainView: Oliveira Jr, PPM; Fischl, Bruce; Amaro, Edson Teaching neuroanatomy using Iphone and IPad. In: Human Brain Mapping, 2011, Quebec, CA. Proc. Human Brain Mapping 2011, 2011. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com http://www.netfilter.com.br ___ 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] How to get surface-based AAL template
Dear Br: Thanks for your help. I have downloaded Colin 27 subject, and the Surfrend toolbox. But I still have some questions about the process. 1. You said I need transform the Colin 27 to the latest FS version (v.5.2). But i don't know how to do this. It is helpful if you can provide some information. 2. How does the Colin 27 space differs from fsaverage MNI305 space? The group analysis of cortical thickness is conducted in fsaverage space, after importing AAL ROI into Colin 27 space, should i transform the obtained ROI into fsaverage space? 3. i don't understand what is the register.dat between COlin 27 and SPM-s single subject t1.nii used for? I have tried the Surfrend, and found there was no entry for input of register file during the processing. Looking forward to your reply. Best wishes. zhiliang At 2013-03-27 13:29:01,Garikoitz Lerma-Usabiaga gariko...@gmail.com wrote: Hi, In my case transformation to fsaverage did not work very well. What I did was: - from Surfrend page download Colin 27 subject and transform it to the latest version (now 5.2) - with bbregister obtain register.dat between this Colin 27 subject and SPM-s single subject t1.nii, which is the 2mm version of Colin 27. AAL-s are defined in Colin 27. As they are the same subject, the registering is very good. - now you can import every AAL ROI (in .nii form) to an annotation or in the form of individual labels to your FS Colin 27, using the newly created registering file. - now you can use surf2surf or label2label to go to your subjects and obtain stats. Br! On 27/03/2013, at 05:35, ZhiLiangLong lagosslong1...@163.com wrote: Hi all; I need a suface-based aal template which is compatible with FS surface file. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI space onto the surface template (e.g. fsaverage template) in FS. Is it correct? if in this case, how can i do the transformation? Any suggestions appreciated. Besh wishes. ___ 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] getting started with ROI labels
Hi Fred the first thing to do is run recon-all on a good T1-weighted anatomical from each of your subjects. You can then use mri_label2label to map the labels from one subject onto another. good luck Bruce On Wed, 27 Mar 2013, Fred Lado wrote: Dear Freesurfers,I'm interested in using FS identified labels, such as Brodman areas in the anatomical volume, to measure a feature, say mean intensity in V1, in a second volume registered to the first. I'm new to the use of labels, so some advice on where to start would be appreciated. Thanks, Fred Lado, MD PhD Director, Neurology Service - Moses North Divisions Director, EEG Laboratory Associate Clinical Professor of Neurology Montefiore Medical Center 718-920-8499 office 718-324-3730 fax email: fl...@montefiore.org Confidentiality Notice: This document is protected by EDUCATIONAL LAW 6527 PUBLIC HEALTH LAW 2085, J, K, L, M. This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited and may be unlawful. If you are not the intended recipient, please delete this e-mail immediately. ___ 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] Xhemi stat questions
That makes much more sense than the thing I was looking for.Now I have a problem reading the lh.lh-rh.thickness.mgh with the load_mgh.m function, as I have no idea of how to read it to get the vertex by vertex thickness value of each subject.I tryed as [thick, ~,~,~]=load_mgh('file.mgh',[],[1:nSubjs])then reading: subjIDthick=thick(vtxID,1,1,subjID);where vtxID es the vertex of the .label file I want, and subjID is the number of the subject.is that correct?All this is because I will use it as a covariate in the statistical analysis as suggested in http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27129.htmlRegards,Gabriel.El 26/03/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:Unless you specifically need them for an individual, you should get them from lh.lh-rh.thickness.mgh because that data is sampled onto the symmetric template and so should be unbiased (ie, it will not systematically favor lh or rh).dougOn 03/26/2013 12:40 PM, Gabriel Gonzalez Escamilla wrote: Dear Doug, I meant of a given subject, But, As I'm thinking about this, I'm wondering if it has sense to have left and right cortical thickness of my every individual subjects, or if I should obtain the lh-rh thickness differences for the individuals? I suppose that I should read the lh.lh-rh.thickness.mgh created by mris_preproc to get the average differences in lh-rh hemispheres. Regards, Gabriel El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: Do you mean you want the right hemi thicknesses on the left hemisphere of a given subject or on the fsaverage_sym? doug On 03/25/2013 11:25 AM, Gabriel Gonzalez Escamilla wrote: Thank you, so I'm keeping the one I had. Sorry for my bad explanation. When I do a normal cortical thickness study, I know the average thickness for a label, e.g. cortex, and the values at each vertex of each hemisphere are stored in $subject/surf/?l.thickness. I would like to know if it is possible to obtain the same cortical thickness measure from the lh-rh registered hemispheres of each subject.Regards, GabrielEl 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: On 03/25/2013 10:52 AM, Gabriel Gonzalez Escamilla wrote: Thanks a lot for your answer,I'm sending you attached the diff of the two mris_preproc. Those differences are just added features and won't change your results.When I wrote CT, I was meaning cortical thickness, as normally this values are in surf/?h.thickness, But how do I know the Xhemi-registered thickness values of each subject for lh-rh, or area or any of those indices? I'm not sure what you mean. When you run mris_preproc, you specify whether you want thickness, etc. dougRegards, Gabriel El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió:On 03/22/2013 06:45 AM, Gabriel Gonzalez Escamilla wrote: Dear Doug, I've seen that you restore the files to download, for the Xhemi registration. While I'm checking for the statistical process, I've seen that the one I have is: Date: 2012/12/06 16:06:52, Revision: 1.59.2.4, and the one that is on your ftp server is Date: 2012/12/06 16:06:17, Revision: 1.66, So mine is a lower version but recent hour, and the actual is newer version but seems that was created before the one I have. My question is, Which one should I keep? Can you send me a diff of the two files? If I change the mris_precproc version. Shall I re-run this step before statistical analyses, to create a new lh.lh-rh.thickness.sm00.mgh? On the other hand I have some doubts about the statistical procedure. It's supposed that if I apply the Xhemi registration, as result the left and right hemispheres are equals to each other on every subject, so: A) Where can I get the CT values after the Xhemi registration to FSaverage_sym for the left and right hemispheres? what are CT values? B) Given that I have two groups, Patients and Control, with two levels each, i.e male-female (Gp1male Gp1female Gp2male Gp2female Gp1maleVar1 Gp1femaleVar1 Grp2maleVar1 Grp2femaleVar1), and that I can set the contrasts and fsgd files as with a normal CT analisis, but only on my lh.lh-rh.thickness.smXX.mgh, wich is suppose to contain the left-right differences across subjects, right? Wich would be the right interpretation? of: The interpretation does not really change because it is a xhemi analysis 1) 5 .5 -.5 -.5 0 0 0 0 Is the L-R difference between Grp1 and Grp2 different than 0 (regressing out Var1 and gender) 2) 5 -.5 .5 -.5 0 0 0 0 Is the L-R difference between Males and Females different than 0 (regressing out Var1 and Group) 3) 0 0 0 0 .5 .5 -.5 -.5 Does the slope of the L-R difference with Var1 differ between Grp1 and Grp2(regressing out gender) 4) 0 0 0 0 5 -.5 .5 -.5 Does the slope of the L-R difference with Var1 differ between Male and Female(regressing out group) Many thanks in advanced.
Re: [Freesurfer] Incomplete and poorly formed tracts
Hi Anastasia, I'm attaching the graphic I arrived at with the command: freeview -tv subjectID/dlabel/diff/aparc+aseg.flt.nii.gz -v subjectID/dmri/dtifit_FA.nii.gz Here, I used the subject I send you (Sa69845.5) for the subjectID. I could not detect spill over in these images, mostly because the frontal lobe is a little cut off. Did you perhaps use a different viewer? I'm hoping to be able to detect these mis-registrations better for myself in the future. Thanks for all your help! Sincerely, Susie Kuo NIH On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - Everything under dlabel/diff is mapped to DWI space (either with flirt or with bbregister, whichever you use). The one in my screenshot was dlabel/diff/aparc+aseg.flt.**nii.gz. a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn't end up with the same images as you, however. Can you tell me which images you used to obtain this overlay? I am going to run bbregister tonight, and I'll let you know how it goes -- I'm hopeful! Thank you again! Susie Kuo NIH On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - I'm attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles. I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all. Hope this helps, a.y On Tue, 26 Mar 2013, Susan Kuo wrote: Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that. Thank you, btw, for your very prompt reply yesterday- it was much appreciated! Sincerely, Susie Kuo NIH On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration. a.y On Mon, 25 Mar 2013, Susan Kuo wrote: Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these spotty tracts? Thank you for all your help! -- Susie Kuo NIH The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Susie Kuo Mediocrity knows nothing higher than
Re: [Freesurfer] Incomplete and poorly formed tracts
Hi Susie - The -tv (tract volume) option of freeview is designed specifically to display the merged*.mgz output files of tracula. For a regular volume, use -v or no option at all. For best displaying the aparc+aseg, select it in freeview and choose Lookup Table from the Color map menu. Hope this helps, a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I'm attaching the graphic I arrived at with the command: freeview -tv subjectID/dlabel/diff/aparc+aseg.flt.nii.gz -v subjectID/dmri/dtifit_FA.nii.gz Here, I used the subject I send you (Sa69845.5) for the subjectID. I could not detect spill over in these images, mostly because the frontal lobe is a little cut off. Did you perhaps use a different viewer? I'm hoping to be able to detect these mis-registrations better for myself in the future. Thanks for all your help! Sincerely, Susie Kuo NIH On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - Everything under dlabel/diff is mapped to DWI space (either with flirt or with bbregister, whichever you use). The one in my screenshot was dlabel/diff/aparc+aseg.flt.nii.gz. a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn't end up with the same images as you, however. Can you tell me which images you used to obtain this overlay? I am going to run bbregister tonight, and I'll let you know how it goes -- I'm hopeful! Thank you again! Susie Kuo NIH On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - I'm attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles. I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all. Hope this helps, a.y On Tue, 26 Mar 2013, Susan Kuo wrote: Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that. Thank you, btw, for your very prompt reply yesterday- it was much appreciated! Sincerely, Susie Kuo NIH On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration. a.y On Mon, 25 Mar 2013, Susan Kuo wrote: Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and
Re: [Freesurfer] surf2vol
Sorry, I meant does the left_frontal_lobe.gii overlay properly on the orig volume? doug On 03/27/2013 04:41 AM, Daniel Lumsden wrote: Doug The .nii.gz file is completely empty and doesn't come up on any viewer (fslview, tkmedit, freeview, mricron etc). The .gi files I've generated appear to be tracking in probtrackx (though slowly on my laptop - probably not expected given the sizes of the surfaces). I can also generate binary volumetric masks from the labels using mri_binarize (though they are a little bit speckled - with scattered blank voxels). On my installation I'm having some intermittent difficulties with tkmedit and tksurfer (not consistently opening, sometimes coming up with bus error). Freeview is opening consistently though. I'm not sure if this could be having an affect but I was planning on reinstalling freesurfer today to see if that fixed it. Thank you again for your help Dan Does leftfrontallobe.nii.gz overlay properly in tkmedit? eg, tkmedit subject orig.mgz -surfs -overlay leftfrontallobe.nii.gz -fminmax .5 1 doug On 03/26/2013 07:20 AM, Daniel Lumsden wrote: Bruce Many thanks - that's given me a lot more guidance. Following the help, i've put together the command below: mri_surf2vol --hemi lh --template path to/orig.mgz --outvol path to where I want the file/leftfrontallobe.nii.gz --surfval path to/left_frontal_lobe.gii --fillribbon --volregidentity mov07 Where mov07 is my subjid and left_frontal_lobe.gii is the surface I've generated from the label files to run in probtrakx. This command runs, but produces and empty nifti file. I've changed the output to .mgz with similar effect. I've substituted the rawavg.mgz file for the orig.mgz file, and tried both .nii.gz and .mgz versions of both files and still get an empty output file. The subject is in my $SUBJECTS_DIR. Is there a way to check the .gii files? I generated them using label2surf, having used mris_convert to convert the lh.white and rh.white files from the surf folder for my subject to lh.white.asc and rh.white.asc. Thank you again for your help. Dan Date: Mon, 25 Mar 2013 14:59:28 -0400 From: fis...@nmr.mgh.harvard.edu To: doclums...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surf2vol Hi Dan try using mri_surf2vol instead (it has a much bigger help, thanks to Doug0 Bruce On Mon, 25 Mar 2013, Daniel Lumsden wrote: Dear All Apologies for what I'm sure is a very basic question. I'm new to using freesurfer, and would like to generate cortical parcellations for running in probtrakx. I have followed the instructions from various sources and have managed to generate the parcellations from recon-all, extract the label files from the parcellation, then use mri_mergelabels and label2surf to generate the the .gii files needed for probtrakx. I'd like to be able to display the surface files for illustrative purposes, but I'm struggling to apply the surf2vol command. From the terminal window I can see that the commands required are: surf2vol surf refvol outvol convention I presume that surf is the .gii file I'm trying to visualise, and outvol is to specify the name of the output volume the command will generate, but what should I be using as the refvol? I would be very grateful for any guidance. Please accept my apologies if I've missed a very obvious online explanation for this and thank you in advance. Dan Lumsden Clinical Research Fellow 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 -- 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: 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358
Re: [Freesurfer] Question regarding the subject directory
Hi Luke, people generally use a different SUBJECTS_DIR than the default FS folder. You can create symbolic links to subjects in the default FS folder, but recon-all will do this for you. doug On 03/27/2013 07:53 AM, lukas.sch...@ukb.uni-bonn.de wrote: Hi folks! I would like to use a different subject dirctory (setenv SUBJECTS_DIR full path to subject dir). Does freesurfer still finds the folders which are located in the default subjects directory of the FS installation? Or are they simply not needed for the recon-all process ? I refer to cvs_avg35 etc. not to the test data sets. Please excuse if this question is stupid ... but considering the processsing time ... Many thanks in advance, Luke ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the 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] Incomplete and poorly formed tracts
Hi Anastasia, Thank you! I can see that the aparc+aseg spilled over badly. I am going to try bbregister, and then re-betting (Brain Extraction Tool-ing) the original image, since the dtifit_FA looks to include non-brain near the frontal lobe. I'll keep you and the FS community updated on the results, in case anybody is curious. Sincerely, Susie Kuo NIH On Wed, Mar 27, 2013 at 10:41 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - The -tv (tract volume) option of freeview is designed specifically to display the merged*.mgz output files of tracula. For a regular volume, use -v or no option at all. For best displaying the aparc+aseg, select it in freeview and choose Lookup Table from the Color map menu. Hope this helps, a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I'm attaching the graphic I arrived at with the command: freeview -tv subjectID/dlabel/diff/aparc+**aseg.flt.nii.gz -v subjectID/dmri/dtifit_FA.**nii.gz Here, I used the subject I send you (Sa69845.5) for the subjectID. I could not detect spill over in these images, mostly because the frontal lobe is a little cut off. Did you perhaps use a different viewer? I'm hoping to be able to detect these mis-registrations better for myself in the future. Thanks for all your help! Sincerely, Susie Kuo NIH On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - Everything under dlabel/diff is mapped to DWI space (either with flirt or with bbregister, whichever you use). The one in my screenshot was dlabel/diff/aparc+aseg.flt.**nii.gz. a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn't end up with the same images as you, however. Can you tell me which images you used to obtain this overlay? I am going to run bbregister tonight, and I'll let you know how it goes -- I'm hopeful! Thank you again! Susie Kuo NIH On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - I'm attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles. I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all. Hope this helps, a.y On Tue, 26 Mar 2013, Susan Kuo wrote: Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that. Thank you, btw, for your very prompt reply yesterday- it was much appreciated! Sincerely, Susie Kuo NIH On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration.
Re: [Freesurfer] Incomplete and poorly formed tracts
Actually the brain mask used on the diffusion data *is* the aparc+aseg mapped to diffusion space, so the reason you see that extra non-brain stuff in the FA map is because the aparc+aseg was not aligned well to it. So you just need to switch on bbregister and switch off flirt in your configuration file, and then rerun trac-all. If the DWI-to-T1 registration is good, then the masking issue will be solved too. Good luck! a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, Thank you! I can see that the aparc+aseg spilled over badly. I am going to try bbregister, and then re-betting (Brain Extraction Tool-ing) the original image, since the dtifit_FA looks to include non-brain near the frontal lobe. I'll keep you and the FS community updated on the results, in case anybody is curious. Sincerely, Susie Kuo NIH On Wed, Mar 27, 2013 at 10:41 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - The -tv (tract volume) option of freeview is designed specifically to display the merged*.mgz output files of tracula. For a regular volume, use -v or no option at all. For best displaying the aparc+aseg, select it in freeview and choose Lookup Table from the Color map menu. Hope this helps, a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I'm attaching the graphic I arrived at with the command: freeview -tv subjectID/dlabel/diff/aparc+aseg.flt.nii.gz -v subjectID/dmri/dtifit_FA.nii.gz Here, I used the subject I send you (Sa69845.5) for the subjectID. I could not detect spill over in these images, mostly because the frontal lobe is a little cut off. Did you perhaps use a different viewer? I'm hoping to be able to detect these mis-registrations better for myself in the future. Thanks for all your help! Sincerely, Susie Kuo NIH On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - Everything under dlabel/diff is mapped to DWI space (either with flirt or with bbregister, whichever you use). The one in my screenshot was dlabel/diff/aparc+aseg.flt.nii.gz. a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn't end up with the same images as you, however. Can you tell me which images you used to obtain this overlay? I am going to run bbregister tonight, and I'll let you know how it goes -- I'm hopeful! Thank you again! Susie Kuo NIH On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - I'm attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles. I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all. Hope this helps, a.y On Tue, 26 Mar 2013, Susan Kuo wrote: Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown',
Re: [Freesurfer] surf2vol
Doug When I try to overlay the .gii files on the orig volume I get the following message: Either this surface does not contain valid volume geometry information, or freeview failed to read the information. This surface may not align with volumes and other surfaces I presume this means there is a problem with how I've generated the .gi files? I'm happy the lh.anatomicalregion.label files are working fine because I can generate volumetric masks from them. To get the .gii files I've taken the rh.white and lh.white from the surf folder and copied them into the folder I'm running the terminal in. I'm then using the command: mris_convert rh.white rh.white.asc Then: echo lh.frontallobe.label left_frontal_lobe.txt (which checking gives me a text file of that name with one line, lh.frontallobe.label) Then: label2surf -s lh.white.asc -l left_frontal_lobe.txt -o left_frontal_lobe.gii All of the named files are in the same folder. Thank you again. Confusingly, it does seem like probtrackx is doing something with the .gii files! Dan Sorry, I meant does the left_frontal_lobe.gii overlay properly on the orig volume? dougOn 03/27/2013 04:41 AM, Daniel Lumsden wrote: Doug The .nii.gz file is completely empty and doesn't come up on any viewer (fslview, tkmedit, freeview, mricron etc). The .gi files I've generated appear to be tracking in probtrackx (though slowly on my laptop - probably not expected given the sizes of the surfaces). I can also generate binary volumetric masks from the labels using mri_binarize (though they are a little bit speckled - with scattered blank voxels). On my installation I'm having some intermittent difficulties with tkmedit and tksurfer (not consistently opening, sometimes coming up with bus error). Freeview is opening consistently though. I'm not sure if this could be having an affect but I was planning on reinstalling freesurfer today to see if that fixed it. Thank you again for your help Dan Does leftfrontallobe.nii.gz overlay properly in tkmedit? eg, tkmedit subject orig.mgz -surfs -overlay leftfrontallobe.nii.gz -fminmax .5 1 doug On 03/26/2013 07:20 AM, Daniel Lumsden wrote: Bruce Many thanks - that's given me a lot more guidance. Following the help, i've put together the command below: mri_surf2vol --hemi lh --template path to/orig.mgz --outvol path to where I want the file/leftfrontallobe.nii.gz --surfval path to/left_frontal_lobe.gii --fillribbon --volregidentity mov07 Where mov07 is my subjid and left_frontal_lobe.gii is the surface I've generated from the label files to run in probtrakx. This command runs, but produces and empty nifti file. I've changed the output to .mgz with similar effect. I've substituted the rawavg.mgz file for the orig.mgz file, and tried both .nii.gz and .mgz versions of both files and still get an empty output file. The subject is in my $SUBJECTS_DIR. Is there a way to check the .gii files? I generated them using label2surf, having used mris_convert to convert the lh.white and rh.white files from the surf folder for my subject to lh.white.asc and rh.white.asc. Thank you again for your help. Dan Date: Mon, 25 Mar 2013 14:59:28 -0400 From: fis...@nmr.mgh.harvard.edu To: doclums...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surf2vol Hi Dan try using mri_surf2vol instead (it has a much bigger help, thanks to Doug0 Bruce On Mon, 25 Mar 2013, Daniel Lumsden wrote: Dear All Apologies for what I'm sure is a very basic question. I'm new to using freesurfer, and would like to generate cortical parcellations for running in probtrakx. I have followed the instructions from various sources and have managed to generate the parcellations from recon-all, extract the label files from the parcellation, then use mri_mergelabels and label2surf to generate the the .gii files needed for probtrakx. I'd like to be able to display the surface files for illustrative purposes, but I'm struggling to apply the surf2vol command. From the terminal window I can see that the commands required are: surf2vol surf refvol outvol convention I presume that surf is the .gii file I'm trying to visualise, and outvol is to specify the name of the output volume the command will generate, but what should I be using as the refvol? I would be very grateful for any guidance. Please accept my apologies if I've missed a very obvious online explanation for this and thank you in advance. Dan Lumsden Clinical Research Fellow 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
Re: [Freesurfer] Incomplete and poorly formed tracts
Hi Anastasia, I saved out some of the completed trac-all.cmds following each TRACULA 'step', and I see where aparc+aseg is mapped to diffusion space. Thank you again for all your help - my project is starting to look a lot better! Sincerely, Susie Kuo NIH On Wed, Mar 27, 2013 at 12:02 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Actually the brain mask used on the diffusion data *is* the aparc+aseg mapped to diffusion space, so the reason you see that extra non-brain stuff in the FA map is because the aparc+aseg was not aligned well to it. So you just need to switch on bbregister and switch off flirt in your configuration file, and then rerun trac-all. If the DWI-to-T1 registration is good, then the masking issue will be solved too. Good luck! a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, Thank you! I can see that the aparc+aseg spilled over badly. I am going to try bbregister, and then re-betting (Brain Extraction Tool-ing) the original image, since the dtifit_FA looks to include non-brain near the frontal lobe. I'll keep you and the FS community updated on the results, in case anybody is curious. Sincerely, Susie Kuo NIH On Wed, Mar 27, 2013 at 10:41 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - The -tv (tract volume) option of freeview is designed specifically to display the merged*.mgz output files of tracula. For a regular volume, use -v or no option at all. For best displaying the aparc+aseg, select it in freeview and choose Lookup Table from the Color map menu. Hope this helps, a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I'm attaching the graphic I arrived at with the command: freeview -tv subjectID/dlabel/diff/aparc+** aseg.flt.nii.gz -v subjectID/dmri/dtifit_FA.**nii.gz Here, I used the subject I send you (Sa69845.5) for the subjectID. I could not detect spill over in these images, mostly because the frontal lobe is a little cut off. Did you perhaps use a different viewer? I'm hoping to be able to detect these mis-registrations better for myself in the future. Thanks for all your help! Sincerely, Susie Kuo NIH On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - Everything under dlabel/diff is mapped to DWI space (either with flirt or with bbregister, whichever you use). The one in my screenshot was dlabel/diff/aparc+aseg.flt.**nii.gz. a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn't end up with the same images as you, however. Can you tell me which images you used to obtain this overlay? I am going to run bbregister tonight, and I'll let you know how it goes -- I'm hopeful! Thank you again! Susie Kuo NIH On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - I'm attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles. I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all. Hope this helps, a.y On Tue, 26 Mar 2013, Susan Kuo wrote: Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical
[Freesurfer] June course on structural and functional connectivity at the Martinos Center
Dear Freesurfistas - This new course, offered at the Martinos Center right before the OHBM meeting, may be of interest to some of you. There are some open spots left. For info on how to register and a tentative schedule, see the web page at the end of the announcement. a.y --- STRUCTURAL AND FUNCTIONAL BRAIN CONNECTIVITY AS REVEALED BY MRI Dates: June 3-7, 2013 Themes: Resting State Functional Connectivity and DTI/DSI/Tractography Location: Martinos Center for Biomedical Imaging of the Massachusetts General Hospital; Boston/Charlestown Massachusetts Program Director: Robert L. Savoy In December 2012 the Martinos Center for Biomedical Imaging introduced a new, 5-day program on functional and structural connectivity using MRI. The next edition of this program will be held June 3-7 (two weeks prior to the Organization for Human Brain Mapping annual meeting). There is likely to be an additional program in 2013, to be held near the end of October or early November, 2013. Issues associated with connectivity in the human brain are of increasing importance, as reflected in the large number of abstracts, research articles, and even entire journals devoted to this area, as well as the increased emphasis on lesions within the white matter as being a source of many neuro-psychiatric disorders. MRI has proven to be a valuable tool for examining connectivity both in terms of the coordinated activities of neural networks (using BOLD-based fMRI data collected during rest and during tasks) and also in terms of the structural anatomy of white matter pathways of the brain (using Diffusion Tensor Imaging (DTI), Diffusion Spectrum Imaging (DSI), and tractography programs to analyze and visualize the resulting data). Participants will learn about the technical challenges in acquisition, data processing and visualization of brain networks via the data from fMRI during the so-called resting state, but also available during experimenter-initiated cognitive tasks. Participants will also receive a firm grounding in the power and limitations associated with using diffusion-sensitive MRI to detect and organize the anatomical structure of white matter tracts in the living human brain. The primary goal of this program is to give researchers and clinicians a good start for their investigations using these tools. In that sense, it serves a purpose analogous to that of the Functional MRI Visiting Fellowship Program (fMRIVFP) also offered at the Martinos Center, except that the domain will be structural and functional connectivity of myelinated fiber tracts within the living human brain. The active component of the program will be the use of software tools to promote quality assurance in the data, detect outliers and other problematic attributes of the data, optimize data acquisition, and flexibly visualize the data in the service of asking and answering specific questions. Participants will be expected (though not required) to bring a suitable laptop computer for engaging in the hands-on exercises of the program. There will also be a section on the Connectome MRI Machine that uses exceptionally strong gradients to enhance data acquisition of strutural and functional images. The core faculty is drawn from the staff of the Athinoula A. Martinos Center (of the Massachusetts General Hospital and Massachusetts Institute of Technology) and affiliated faculty from Harvard University, McLean Hospital and other local institutions. Guest lecturers (at the Dec, 2012 program) included faculty from the Child Mind Institute of New York, NIH, Stanford University, The Donders Institute, the University of Cambridge and others. For questions, e-mail: fmri...@nmr.mgh.harvard.edu For more information and registration, see: http://martinos.org/ConnectivityCourse___ 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] CT as covariate
Dear Freesurfers I will introduce the mean cortial thickness as covariate into my statistical model, but I'm wonderind which way will be the best. To get the cortical thickness in individual space, or in AVG space? Thank you all in advanced, Rafa. ___ 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] tractstats@table output oddity
I ran tractstats2table to make a table of my dti tract stats for the fmajor_PP tract see the attached script file @tractstats2table and the file list fmajor_file_list.txt it produced the output file fmajor_table.txt (attached) in the output table all the values for the variables are the same for the 7 rows. the values are from last file in the list DTItracts/1276/fmajor_PP_avg23_mni_flt/pathstats.overall.txt why is this? input files have different values for the various variable Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 @tractstats2table Description: Binary data DTItracts/1069/fmajor_PP_avg23_mni_flt/pathstats.overall.txt DTItracts/1167/fmajor_PP_avg23_mni_flt/pathstats.overall.txt DTItracts/1191/fmajor_PP_avg23_mni_flt/pathstats.overall.txt DTItracts/1248/fmajor_PP_avg23_mni_flt/pathstats.overall.txt DTItracts/1252/fmajor_PP_avg23_mni_flt/pathstats.overall.txt DTItracts/1267/fmajor_PP_avg23_mni_flt/pathstats.overall.txt DTItracts/1276/fmajor_PP_avg23_mni_flt/pathstats.overall.txt fmajor Count Volume Len_Min Len_Max Len_Avg Len_Center AD_Avg AD_Avg_Weight AD_Avg_Center RD_Avg RD_Avg_Weight RD_Avg_Center MD_Avg MD_Avg_Weight MD_Avg_Center FA_Avg FA_Avg_Weight FA_Avg_Center freesurfer 1000.0 144.0 29.050.036.896 34.00.00133574 0.00136416 0.00126968 0.000659806 0.000681595 0.000547329 0.000885118 0.000909116 0.000788114 0.4350630.433158 0.486111 freesurfer 1000.0 144.0 29.050.036.896 34.00.00133574 0.00136416 0.00126968 0.000659806 0.000681595 0.000547329 0.000885118 0.000909116 0.000788114 0.4350630.433158 0.486111 freesurfer 1000.0 144.0 29.050.036.896 34.00.00133574 0.00136416 0.00126968 0.000659806 0.000681595 0.000547329 0.000885118 0.000909116 0.000788114 0.4350630.433158 0.486111 freesurfer 1000.0 144.0 29.050.036.896 34.00.00133574 0.00136416 0.00126968 0.000659806 0.000681595 0.000547329 0.000885118 0.000909116 0.000788114 0.4350630.433158 0.486111 freesurfer 1000.0 144.0 29.050.036.896 34.00.00133574 0.00136416 0.00126968 0.000659806 0.000681595 0.000547329 0.000885118 0.000909116 0.000788114 0.4350630.433158 0.486111 freesurfer 1000.0 144.0 29.050.036.896 34.00.00133574 0.00136416 0.00126968 0.000659806 0.000681595 0.000547329 0.000885118 0.000909116 0.000788114 0.4350630.433158 0.486111 freesurfer 1000.0 144.0 29.050.036.896 34.00.00133574 0.00136416 0.00126968 0.000659806 0.000681595 0.000547329 0.000885118 0.000909116 0.000788114 0.4350630.433158 0.486111 ___ 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] CT as covariate
I don't think it would make a difference, but I would use the individual space. doug On 03/27/2013 01:12 PM, Rafa X wrote: Dear Freesurfers I will introduce the mean cortial thickness as covariate into my statistical model, but I'm wonderind which way will be the best. To get the cortical thickness in individual space, or in AVG space? Thank you all in advanced, Rafa. ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the 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] Problems with recon-all--won't generate wm or surf files
Hello, I've been having problems with recon-all for only 1 of my 50 subjects. Recon-all is failing somehow before white matter or surf files are generated. The T1 and nu.mgz files look fine. Below are the files that my subject is missing in the 'mri' subdirectory (they are also missing the entire surfs directory): filled.mgz lh.ribbon.mgz rh.ribbon.mgz ribbon.mgz wm.asegedit.mgz wm.mgz wmparc.mgz Below is the last few lines of output from my recon-all log file: #@# WM Segmentation Tue Mar 26 18:09:32 EDT 2013 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 104.6 +- 4.9 [80.0 -- 125.0] GM (72.0) : 69.4 +- 10.8 [30.0 -- 96.0] setting bottom of white matter range to 80.2 setting top of gray matter range to 91.0 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 5962 sparsely connected voxels removed... thickening thin strands 20 segments, 3294 filled 117 bright non-wm voxels segmented. 4879 diagonally connected voxels added... white matter segmentation took 3.4 minutes writing output to wm.seg.mgz... changing input type from 3 to UCHAR mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... mri_edit_wm_with_aseg: volume brain.mgz must be MRI_UCHAR reading wm segmentation from wm.seg.mgz... Linux ncfc21.rc.fas.harvard.edu 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:45:44 EST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s M87190691 exited with ERRORS at Tue Mar 26 18:12:57 EDT 2013 For more details, see the log file /ncf/jwb/studies/PrisonReward/Active/Analyses/fsrecon_n49_01252013_qdec/M87190691/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting make: *** [/ncf/jwb/studies/PrisonReward/Active/Analyses/fsrecon_n49_01252013_qdec/M87190691/mri/wm.mgz] Error 1 Any ideas as to what might be failing? Thanks for your help! Hayley ___ 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] Problems with recon-all--won't generate wm or surf files
Hi Hayley I think the problem is that the nu.mgz I gave you has a voxel type of float (3) instead of uchar (0). You will need to figure out which volumes are float with mri_info, and convert each of them to uchar with: mri_convert -odt uchar -ns 1 float.mgz uchar.mgz where the -ns 1 flag tells it not to scale the intensities. Sorry, I should have thought of this before sending you the updated nu.mgz. Make sure all the uchar volumes are named as we expect them Bruce On Wed, 27 Mar 2013, Hayley Dorfman wrote: Hello, I've been having problems with recon-all for only 1 of my 50 subjects. Recon-all is failing somehow before white matter or surf files are generated. The T1 and nu.mgz files look fine. Below are the files that my subject is missing in the 'mri' subdirectory (they are also missing the entire surfs directory): filled.mgz lh.ribbon.mgz rh.ribbon.mgz ribbon.mgz wm.asegedit.mgz wm.mgz wmparc.mgz Below is the last few lines of output from my recon-all log file: #@# WM Segmentation Tue Mar 26 18:09:32 EDT 2013 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 104.6 +- 4.9 [80.0 -- 125.0] GM (72.0) : 69.4 +- 10.8 [30.0 -- 96.0] setting bottom of white matter range to 80.2 setting top of gray matter range to 91.0 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 5962 sparsely connected voxels removed... thickening thin strands 20 segments, 3294 filled 117 bright non-wm voxels segmented. 4879 diagonally connected voxels added... white matter segmentation took 3.4 minutes writing output to wm.seg.mgz... changing input type from 3 to UCHAR mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... mri_edit_wm_with_aseg: volume brain.mgz must be MRI_UCHAR reading wm segmentation from wm.seg.mgz... Linux ncfc21.rc.fas.harvard.edu 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:45:44 EST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s M87190691 exited with ERRORS at Tue Mar 26 18:12:57 EDT 2013 For more details, see the log file /ncf/jwb/studies/PrisonReward/Active/Analyses/fsrecon_n49_01252013_qdec/M87190691/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting make: *** [/ncf/jwb/studies/PrisonReward/Active/Analyses/fsrecon_n49_01252013_qdec/M87190691/mri/wm.mgz] Error 1 Any ideas as to what might be failing? Thanks for your help! Hayley ___ 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] memory allocation errors on Snow Leopard running dmri_train
Hi Ping - Can you send us your entire trac-all.log? There's some info in there about your system and the freesurfer build you're using that we'll need to try to replicate the problem. Thanks, a.y On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: Hi Anastasia, It had the same issue before, but worked fine after installing the fixed dmri patch for Snow Leopard. Thanks. ping On Tue, Mar 26, 2013 at 5:09 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - Are you running this on the same system where you were running the 5.1 snow leopard build without a problem? a.y On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: Hi FS users, I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into errors. The 5.2 recon-all of T1 was finished ok. Here is the final part of log file. #@# Priors Tue Mar 26 14:39:36 EDT 2013 /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni/aparc+aseg_mask.nii.gz --fa /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/dtifit_FA.nii.gz --cptdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/diff --reg /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/xfms/mni2diff.flt.mat --ncpts 10 --trunc cwd /Users/twbrkmp2 cmdline /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk
[Freesurfer] question regarding creating Brodmann area
Dear. freesurfer users. I'm trying to make a label for Brodmann area 44. According to the freesurfer manual, I've run, recon-all -s subjid -ba-labels However, it says Flag -ba-labels unrecognized. I'm using freesurfer version 4.5.0. By default, recon-all is supposed to create Brodmann areas under label directory. However, inside the lable directory, I see only aparc.annot.a2009s.ctab aparc.annot.ctab lh.aparc.a2009s.annot lh.aparc.annot lh.cortex.label rh.aparc.a2009s.annot rh.aparc.annot rh.cortex.label Please leave me any comment!! I appreciate it a lot! Best regards, Ji Won Bang ___ 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] question regarding creating Brodmann area
you will need to upgrade to a newer version - the BA labeling didn't exist in 4.5 On Wed, 27 Mar 2013, Ji Won Bang wrote: Dear. freesurfer users. I'm trying to make a label for Brodmann area 44. According to the freesurfer manual, I've run, recon-all -s subjid -ba-labels However, it says Flag -ba-labels unrecognized. I'm using freesurfer version 4.5.0. By default, recon-all is supposed to create Brodmann areas under label directory. However, inside the lable directory, I see only aparc.annot.a2009s.ctab aparc.annot.ctab lh.aparc.a2009s.annot lh.aparc.annot lh.cortex.label rh.aparc.a2009s.annot rh.aparc.annot rh.cortex.label Please leave me any comment!! I appreciate it a lot! Best regards, Ji Won Bang ___ 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] specifying random effects in LME (Linear Mixed Effects models)
I am following the wiki page for LME analysis and I have a quick question. The Mass-univariate example near the bottom of the page proposes an initial model that contains intercept, linear and quadratic terms as random effects. However, the examples just below for lme_mass_fit_EM_init(), lme_mass_fit_EM_Rgw() only have [1 2] as selected random effects. Should the vector Zcols contain [1 2 3] as selected random effects in order to test the proposed model? Thanks, Francois François Lalonde, Ph.D. Child Psychiatry Branch NIMH / NIH 10 Center Drive, Room 3N202 Bethesda, MD 20892 ___ 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] tractstats@table output oddity
if i do the 7 subjects individually, 1 by 1 with the tractstats2table for each subject, the data in the table are ok, it's just when I process them all with 1 tractsstat2table command, that the data is the same in each row of the output Jon - Original Message - From: Jon Wieser wie...@uwm.edu To: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, March 27, 2013 12:17:40 PM Subject: [Freesurfer] tractstats@table output oddity I ran tractstats2table to make a table of my dti tract stats for the fmajor_PP tract see the attached script file @tractstats2table and the file list fmajor_file_list.txt it produced the output file fmajor_table.txt (attached) in the output table all the values for the variables are the same for the 7 rows. the values are from last file in the list DTItracts/1276/fmajor_PP_avg23_mni_flt/pathstats.overall.txt why is this? input files have different values for the various variable Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ 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. -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] bbregister error with hardi data
Hi Corinna, are you sure that the mri-in-hardi.nii.reg registration is accurate? the following should look in register: tkregister2 --reg mri-in-hardi.nii.reg --mov mri-in-hardi.nii --surfs doug On 03/25/2013 06:09 PM, Corinna Bauer wrote: I am trying to get the V1 label to map onto my HARDI data, however, the mri_label2vol registration is off. The label ends up in the brainstem rather than V1. the V1 labels are in the proper location when I use orig.mgz, but when I used the output from mri_vol2vol as the mri-in-hardi or the hardi itself as the temp image, the location of the label is off. mri_label2vol --label label/rh.V1.label --label label/lh.V1.label --temp mri-in-hardi.nii --reg mri-in-hardi.nii.reg --o lindsay_v1.nii On Mon, Mar 25, 2013 at 4:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: yep, looks right On 03/25/2013 03:12 PM, Corinna Bauer wrote: Also, I now want to apply the inverse transform to move the T1 into the HARDI space. Did I do this correctly? It looks good in tkregister. mri_vol2vol --mov hardi/ffiltered_func_data_01.nii.gz --targ mri/orig.mgz --reg register.dat --inv --o mri-in-hardi.nii On Mon, Mar 25, 2013 at 1:47 PM, Corinna Bauer corinna...@gmail.com mailto:corinna...@gmail.com mailto:corinna...@gmail.com mailto:corinna...@gmail.com wrote: ahhh, yes, that's it. sorry my oversight. On Mon, Mar 25, 2013 at 1:45 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Are you sure you made the right edit? It should be --fsvol $fsvol.mgz It looks like you might have changed it to --fsvol.mgz $fsvol On 03/25/2013 01:30 PM, Corinna Bauer wrote: Ok I adjusted the bbregister file to say fsvol.mgz in the location you specified and got this error a bit later on in the bbregister output: setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/symmetry cd /usr/local/freesurfer/subjects/symmetry/lindsay /usr/local/freesurfer/bin/bbregister --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --dti --init-fsl --reg register.dat $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux lotfi 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15807/template.nii mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15807/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from hardi/ffiltered_func_data_01.nii.gz... TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.991204, -0.025762, 0.129811) j_ras = (-0.0259819, 0.999662, 0) k_ras = (0.129768, 0.00337275, 0.991539) writing to ./tmp.bbregister.15807/template.nii... fslregister --s lindsay --mov ./tmp.bbregister.15807/template.nii --reg ./tmp.bbregister.15807/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15807/fslregister --dof 6 --fsvol.mgz brainmask ERROR: Flag --fsvol.mgz unrecognized. --s lindsay --mov ./tmp.bbregister.15807/template.nii --reg ./tmp.bbregister.15807/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15807/fslregister --dof 6 --fsvol.mgz brainmask mri_segreg --mov ./tmp.bbregister.15807/template.nii --init-reg ./tmp.bbregister.15807/reg.init.dat --out-reg ./tmp.bbregister.15807/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.15807/reg.init.dat mri_segreg --mov ./tmp.bbregister.15807/template.nii --init-reg
Re: [Freesurfer] view retinotopy results in version 5
Hi Yuhong, I put a new version that has a --flat and --patch option here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview I have not tested it because I don't have any retinotopy handy. Can you test it and let me know whether it works? doug On 03/26/2013 03:00 PM, Y.V. Jiang wrote: Hi, I was able to view retinotopic mapping results using rtview in version 5. However, the display was on the inflated surface. Is there a way to view the results on the flattened occipital map, similar to version 4's surf-sess -flat? Thanks! -Yuhong ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the 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: Cortical thickness in average space
what is the size of the 4D matrix? On 03/27/2013 05:41 AM, Rafa X wrote: Thanks Bruce for your answer, as you asked I'm forwarding this question to the list in case any other can answer this. We already have the surface generated by mri_preproc, now we are trying to read it using the matlab function read_mgh. It returns a 4-D matrix, how can we interpret this data to get the cortical thickness values at each vertex of every subject? Rafa Gabi 2013/3/26 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Rafa and Gabi yes, that's pretty much what the -qcache flag does in recon-all. Or you can use mri_surf2surf to do it. cheers Bruce On Tue, 26 Mar 2013, Rafa X wrote: Hi Freesurfers, We would need to obtain the cortical thickness of each subject in the space of the average subject (built from our subject population), Does it exists? If so, Can I use the label files produced by mri_surfcluster to directly extract the mean cortical thickness of each ROI in each subject? We want to avoid to trasform each cluster to every subject. Thank you all in advance, Rafa Gabi. ___ 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 -- 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: 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] Correlation with cortical thickness
In the 2nd option, age and weight (and other variables) are simultaneously fit to the data. Most people refer to this as regressing out the effect of one variable when looking at the other. But it is not regressing out age and then looking at the correlation of age with the residual. doug On 03/27/2013 07:02 AM, Martijn Steenwijk wrote: Dear all, I've a question regarding computing correlations with cortical thicknesses on the surface; Suppose I have two variables for each subject: (age and weight) and I want to compute the correlation between cortical thickness and weight, corrected for age. Option 1: Fsgd contains: Variables weight Contrast file contains: 0 1 Option 2: Fsgd contains: Variables age weight Contrast file contains: 0 0 1 Is it true that the effect of age is regressed out in the second option; and it computes the correlation between CT and weight after correcting for age? Best, Martijn ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the 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] Correlation with cortical thickness
Here is a link describing the difference in the methods: http://onlinelibrary.wiley.com/store/10.1046/j.1365-2656.2002.00618.x/asset/j.1365-2656.2002.00618.x.pdf?v=1t=heswinwbs=dce1a222e16e861d105340fd919c65fb43dc39ac Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Wed, Mar 27, 2013 at 3:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: In the 2nd option, age and weight (and other variables) are simultaneously fit to the data. Most people refer to this as regressing out the effect of one variable when looking at the other. But it is not regressing out age and then looking at the correlation of age with the residual. doug On 03/27/2013 07:02 AM, Martijn Steenwijk wrote: Dear all, I've a question regarding computing correlations with cortical thicknesses on the surface; Suppose I have two variables for each subject: (age and weight) and I want to compute the correlation between cortical thickness and weight, corrected for age. Option 1: Fsgd contains: Variables weight Contrast file contains: 0 1 Option 2: Fsgd contains: Variables age weight Contrast file contains: 0 0 1 Is it true that the effect of age is regressed out in the second option; and it computes the correlation between CT and weight after correcting for age? Best, Martijn ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the 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] Xhemi stat questions
If you use
thick = fast_vol2mat(MRIread('file.mgh'));
thick will be a matrix of nsubjects-by-nvertices.
Note that the vertex indices from labels are 0-based whereas matlab
expects 1-based.
doug
On 03/27/2013 09:08 AM, Gabriel Gonzalez Escamilla wrote:
That makes much more sense than the thing I was looking for.
Now I have a problem reading the lh.lh-rh.thickness.mgh with the
load_mgh.m function, as I have no idea of how to read it to get the
vertex by vertex thickness value of each subject.
I tryed as [thick, ~,~,~]=load_mgh('file.mgh',[],[1:nSubjs])
then reading: subjIDthick=thick(vtxID,1,1,subjID);
where vtxID es the vertex of the .label file I want, and subjID is the
number of the subject.
is that correct?
All this is because I will use it as a covariate in the statistical
analysis as suggested in
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27129.html
Regards,
Gabriel.
El 26/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió:
Unless you specifically need them for an individual, you should get them
from lh.lh-rh.thickness.mgh because that data is sampled onto the
symmetric template and so should be unbiased (ie, it will not
systematically favor lh or rh).
doug
On 03/26/2013 12:40 PM, Gabriel Gonzalez Escamilla wrote:
Dear Doug,
I meant of a given subject,
But, As I'm thinking about this, I'm wondering if it has sense to have
left and right cortical thickness of my every individual subjects, or
if I should obtain the lh-rh thickness differences for the individuals?
I suppose that I should read the lh.lh-rh.thickness.mgh created by
mris_preproc to get the average differences in lh-rh hemispheres.
Regards,
Gabriel
El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió:
Do you mean you want the right hemi thicknesses on the left hemisphere
of a given subject or on the fsaverage_sym?
doug
On 03/25/2013 11:25 AM, Gabriel Gonzalez Escamilla wrote:
Thank you, so I'm keeping the one I had.
Sorry for my bad explanation. When I do a normal cortical thickness
study, I know the average thickness for a label, e.g. cortex,
and the
values at each vertex of each hemisphere are stored in
$subject/surf/?l.thickness. I would like to know if it is
possible to
obtain the same cortical thickness measure from the lh-rh registered
hemispheres of each subject.
Regards,
Gabriel
El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu
escribió:
On 03/25/2013 10:52 AM, Gabriel Gonzalez Escamilla wrote:
Thanks a lot for your answer,
I'm sending you attached the diff of the two mris_preproc.
Those differences are just added features and won't change your
results.
When I wrote CT, I was meaning cortical thickness, as normally
this
values are in surf/?h.thickness, But how do I know the
Xhemi-registered thickness values of each subject for lh-rh, or
area
or any of those indices?
I'm not sure what you mean. When you run mris_preproc, you specify
whether you want thickness, etc.
doug
Regards,
Gabriel
El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu
escribió:
On 03/22/2013 06:45 AM, Gabriel Gonzalez Escamilla wrote:
Dear Doug,
I've seen that you restore the files to download, for the Xhemi
registration. While I'm checking for the statistical
process, I've
seen that the one I have is: Date: 2012/12/06 16:06:52,
Revision:
1.59.2.4, and the one that is on your ftp server is Date:
2012/12/06
16:06:17, Revision: 1.66, So mine is a lower version but
recent hour,
and the actual is newer version but seems that was created
before the
one I have. My question is, Which one should I keep?
Can you send me a diff of the two files?
If I change the mris_precproc version. Shall I re-run this
step
before statistical analyses, to create a new
lh.lh-rh.thickness.sm00.mgh?
On the other hand I have some doubts about the statistical
procedure.
It's supposed that if I apply the Xhemi registration, as
result the
left and right hemispheres are equals to each other on every
subject, so:
A) Where can I get the CT values after the Xhemi
registration to
FSaverage_sym for the left and right hemispheres?
what are CT values?
B) Given that I have two groups, Patients and Control, with two
levels
each, i.e male-female (Gp1male Gp1female Gp2male Gp2female
Gp1maleVar1 Gp1femaleVar1 Grp2maleVar1 Grp2femaleVar1), and
that
I can
set the contrasts and fsgd files as with a normal CT
analisis, but
only on my lh.lh-rh.thickness.smXX.mgh, wich is suppose to
contain the
left-right differences across subjects, right?
Wich would be the right interpretation? of:
The interpretation does not really change because it is a xhemi
analysis
1) 5 .5 -.5
Re: [Freesurfer] surf2vol
it sounds like the problem is in label2surf. Where did that come from? On 03/27/2013 12:09 PM, Daniel Lumsden wrote: Doug When I try to overlay the .gii files on the orig volume I get the following message: Either this surface does not contain valid volume geometry information, or freeview failed to read the information. This surface may not align with volumes and other surfaces I presume this means there is a problem with how I've generated the .gi files? I'm happy the lh.anatomicalregion.label files are working fine because I can generate volumetric masks from them. To get the .gii files I've taken the rh.white and lh.white from the surf folder and copied them into the folder I'm running the terminal in. I'm then using the command: mris_convert rh.white rh.white.asc Then: echo lh.frontallobe.label left_frontal_lobe.txt (which checking gives me a text file of that name with one line, lh.frontallobe.label) Then: label2surf -s lh.white.asc -l left_frontal_lobe.txt -o left_frontal_lobe.gii All of the named files are in the same folder. Thank you again. Confusingly, it does seem like probtrackx is doing something with the .gii files! Dan Sorry, I meant does the left_frontal_lobe.gii overlay properly on the orig volume? doug On 03/27/2013 04:41 AM, Daniel Lumsden wrote: Doug The .nii.gz file is completely empty and doesn't come up on any viewer (fslview, tkmedit, freeview, mricron etc). The .gi files I've generated appear to be tracking in probtrackx (though slowly on my laptop - probably not expected given the sizes of the surfaces). I can also generate binary volumetric masks from the labels using mri_binarize (though they are a little bit speckled - with scattered blank voxels). On my installation I'm having some intermittent difficulties with tkmedit and tksurfer (not consistently opening, sometimes coming up with bus error). Freeview is opening consistently though. I'm not sure if this could be having an affect but I was planning on reinstalling freesurfer today to see if that fixed it. Thank you again for your help Dan Does leftfrontallobe.nii.gz overlay properly in tkmedit? eg, tkmedit subject orig.mgz -surfs -overlay leftfrontallobe.nii.gz -fminmax .5 1 doug On 03/26/2013 07:20 AM, Daniel Lumsden wrote: Bruce Many thanks - that's given me a lot more guidance. Following the help, i've put together the command below: mri_surf2vol --hemi lh --template path to/orig.mgz --outvol path to where I want the file/leftfrontallobe.nii.gz --surfval path to/left_frontal_lobe.gii --fillribbon --volregidentity mov07 Where mov07 is my subjid and left_frontal_lobe.gii is the surface I've generated from the label files to run in probtrakx. This command runs, but produces and empty nifti file. I've changed the output to .mgz with similar effect. I've substituted the rawavg.mgz file for the orig.mgz file, and tried both .nii.gz and .mgz versions of both files and still get an empty output file. The subject is in my $SUBJECTS_DIR. Is there a way to check the .gii files? I generated them using label2surf, having used mris_convert to convert the lh.white and rh.white files from the surf folder for my subject to lh.white.asc and rh.white.asc. Thank you again for your help. Dan Date: Mon, 25 Mar 2013 14:59:28 -0400 From: fis...@nmr.mgh.harvard.edu To: doclums...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surf2vol Hi Dan try using mri_surf2vol instead (it has a much bigger help, thanks to Doug0 Bruce On Mon, 25 Mar 2013, Daniel Lumsden wrote: Dear All Apologies for what I'm sure is a very basic question. I'm new to using freesurfer, and would like to generate cortical parcellations for running in probtrakx. I have followed the instructions from various sources and have managed to generate the parcellations from recon-all, extract the label files from the parcellation, then use mri_mergelabels and label2surf to generate the the .gii files needed for probtrakx. I'd like to be able to display the surface files for illustrative purposes, but I'm struggling to apply the surf2vol command. From the terminal window I can see that the commands required are: surf2vol surf refvol outvol convention I presume that surf is the .gii file I'm trying to visualise, and outvol is to specify the name of the output volume the command will generate, but what should I be using as the refvol? I would be very grateful for any guidance. Please accept my apologies if I've missed a very obvious online explanation for this and thank you in advance. Dan Lumsden Clinical Research Fellow The information in this e-mail is intended only for the person to
Re: [Freesurfer] view retinotopy results in version 5
Hi Doug, It worked very well, thank you so much! For future references, these are the commands I put in with this new version of rtview (under the folder bold): Polar angle: rtview --lh --polar --real rtopy.self.lh/polar/real.nii.gz --imag rtopy.self.lh/polar/imag.nii.gz --fsig rtopy.self.lh/polar/fsig.nii.gz --s MySubjectNameInAnatomicalFolder --flat Eccentricity: rtview --lh --eccen --real rtopy.self.lh/eccen/real.nii.gz --imag rtopy.self.lh/eccen/imag.nii.gz --fsig rtopy.self.lh/eccen/fsig.nii.gz --s MySubjectNameInAnatomicalFolder --flat I compared the results from Version 5's rtview (see above) and Version 4's surf-sess from the same participant. The resulting maps were highly consistent. The only difference is that the colors were more scattered in Version 4, making it harder to identify the borders between regions. -Yuhong On Wed, Mar 27, 2013 at 2:35 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Yuhong, I put a new version that has a --flat and --patch option here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview I have not tested it because I don't have any retinotopy handy. Can you test it and let me know whether it works? doug On 03/26/2013 03:00 PM, Y.V. Jiang wrote: Hi, I was able to view retinotopic mapping results using rtview in version 5. However, the display was on the inflated surface. Is there a way to view the results on the flattened occipital map, similar to version 4's surf-sess -flat? Thanks! -Yuhong ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Use a SPM roi to extract thickness measurements
Hi all, I have been trying to take an SPM volume and extract FS thickness measurements. I think I successfully took my spm volume from mni152 to fsaverage space (mni305) via the command line: mri_vol2vol --mov $FREESURFER_HOME/subjects/fsaverage/mri.2mm/mni305.cor.mgz --targ RTPJ_9mm_001_10_64_-54_16.img --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --inv --o $SUBJECTS_DIR/2506/mri/RTPJ_mni305_9mm_001_10_64_-54_16.nii.gz Then I turned it into an ROI: mri_binarize --i $SUBJECTS_DIR/2506/mri/RTPJ_mni305_9mm_001_10_64_-54_16.nii.gz --o $SUBJECTS_DIR/2506/mri/RTPJ_mni305_roi_9mm_001_10_64_-54_16.nii.gz --min .01 From here I figured I could map it to the fsaverage surface (mri_vol2surf) and extract thickness measurements (mri_segstats using rh.thickness.fsaverage.mgh) as suggested in the volume roi cortical thickness workflow. However, some of my ROIs don't show up after I transform them. From what I can tell, this is because they don't intersect with the fsaverage surface. My thinking was that it might be better to stay within the individual subject space. So I would: 1. transform ROI to subject space 2. extract thickness values from rh.thickness However, I am struggling to get the roi into single subject space. I feel like this transform (or the inverse of it) should exist because I put all my subjects into fsaverage space via the -qcache flag, but i couldn't tell what to use. So I tried: fslregister --s 2506 --mov $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --reg $SUBJECTS_DIR/2506/fsaverage_to_indiv.dat But the registration doesn't look all that good. I am not sure if this is because the fsaverage is 'smoothed' or what. And then I am at a loss for how to put my roi into individual space and then extract thickness, or even if this is the right approach. Thanks, Stephanie ___ 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: Re: memory allocation errors on Snow Leopard running dmri_train (fwd)
Ping, According to line 9 of the log file you sent to Anastasia, are running freesurfer version v5.1. Not version 5.2. -Zeke Original Message Subject: Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train (fwd) Date: Wed, 27 Mar 2013 15:17:34 -0400 (EDT) From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Zeke Kaufman zkauf...@nmr.mgh.harvard.edu -- Forwarded message -- Date: Wed, 27 Mar 2013 13:44:56 -0400 From: Ping-Hong Yeh pinghong...@gmail.com To: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train Hi Anastasia, See the attached. Thank you. ping On Wed, Mar 27, 2013 at 1:38 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - Can you send us your entire trac-all.log? There's some info in there about your system and the freesurfer build you're using that we'll need to try to replicate the problem. Thanks, a.y On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: Hi Anastasia, It had the same issue before, but worked fine after installing the fixed dmri patch for Snow Leopard. Thanks. ping On Tue, Mar 26, 2013 at 5:09 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - Are you running this on the same system where you were running the 5.1 snow leopard build without a problem? a.y On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: Hi FS users, I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into errors. The 5.2 recon-all of T1 was finished ok. Here is the final part of log file. #@# Priors Tue Mar 26 14:39:36 EDT 2013 /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni/aparc+aseg_mask.nii.gz --fa /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/dtifit_FA.nii.gz --cptdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/diff --reg /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/xfms/mni2diff.flt.mat --ncpts 10 --trunc cwd /Users/twbrkmp2 cmdline /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt
Re: [Freesurfer] specifying random effects in LME (Linear Mixed Effects models)
Hi Francois If you want to test the model with three random effects including intercept, time, and time*time as the random effects then you should use [1 2 3] (these are the columns corresponding to those covariates in X). Actually, for the example in the wiki page we first tested [1 2 3] but the model [1 2] was the best at most vertices. In general, you need more than 4 repeated measures to think of including three random effects in the model for the covariance. Otherwise two random effects are usually enough (you can still include time*time in the model for the mean as in the wiki ). Also, computation time increases quickly with the number of random effects. There is an oncoming paper that will expand more on our longitudinal mass-univariate analyses with lme (hopefully soon). Best -Jorge De: Lalonde, Francois (NIH/NIMH) [E] flalo...@mail.nih.gov Para: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Enviado: Miércoles 27 de marzo de 2013 15:20 Asunto: [Freesurfer] specifying random effects in LME (Linear Mixed Effects models) I am following the wiki page for LME analysis and I have a quick question. The Mass-univariate example near the bottom of the page proposes an initial model that contains intercept, linear and quadratic terms as random effects. However, the examples just below for lme_mass_fit_EM_init(), lme_mass_fit_EM_Rgw() only have [1 2] as selected random effects. Should the vector Zcols contain [1 2 3] as selected random effects in order to test the proposed model? Thanks, Francois François Lalonde, Ph.D. Child Psychiatry Branch NIMH / NIH 10 Center Drive, Room 3N202 Bethesda, MD 20892 ___ 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.
[Freesurfer] Admin: Please unsubscribe this email address
Hello Admin, Please unsubscribe this email address. Regards, Manish ___ 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] Admin: Please unsubscribe this email address
Hi Maish, You can just go to https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer and unsubscribe your email address. Lilla On Wed, 27 Mar 2013, Dalwani, Manish wrote: Hello Admin, Please unsubscribe this email address. Regards, Manish ___ 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] memory allocation errors on Snow Leopard running dmri_train (fwd)
Ping, Yes, I see. We are looking into it now and will try and replicate the issue. -Zeke On 03/27/2013 05:21 PM, Ping-Hong Yeh wrote: Hi Zeke, That specific subject had v5.1 recon-all run by Leopard with FS v5.1 (another computer), but v5.2 trac-all run by Snow Leopard with FS v5.2 . If you scroll down the log file, you will see the /Application/freesurfer, which is the v5.2 where it crashed. Anyhow I have attached the log file of another subject run by FS 5.2, both recon-all and trac-all. Thanks. ping On Wed, Mar 27, 2013 at 4:00 PM, zkauf...@nmr.mgh.harvard.edu zkauf...@nmr.mgh.harvard.edu wrote: Ping, According to line 9 of the log file you sent to Anastasia, are running freesurfer version v5.1. Not version 5.2. -Zeke Original Message Subject: Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train (fwd) Date: Wed, 27 Mar 2013 15:17:34 -0400 (EDT) From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Zeke Kaufman zkauf...@nmr.mgh.harvard.edu -- Forwarded message -- Date: Wed, 27 Mar 2013 13:44:56 -0400 From: Ping-Hong Yeh pinghong...@gmail.com To: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train Hi Anastasia, See the attached. Thank you. ping On Wed, Mar 27, 2013 at 1:38 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - Can you send us your entire trac-all.log? There's some info in there about your system and the freesurfer build you're using that we'll need to try to replicate the problem. Thanks, a.y On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: Hi Anastasia, It had the same issue before, but worked fine after installing the fixed dmri patch for Snow Leopard. Thanks. ping On Tue, Mar 26, 2013 at 5:09 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - Are you running this on the same system where you were running the 5.1 snow leopard build without a problem? a.y On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: Hi FS users, I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into errors. The 5.2 recon-all of T1 was finished ok. Here is the final part of log file. #@# Priors Tue Mar 26 14:39:36 EDT 2013 /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz
