[Freesurfer] Fwd: 7T Facility Fellow Position in Brisbane
FYI Original Message Subject:7T Facility Fellow Position in Brisbane Resent-Date:Thu, 14 Mar 2013 01:01:35 -0400 Resent-From:dgr...@partners.org Date: Thu, 14 Mar 2013 04:59:03 + From: Ross Cunnington r.cunning...@uq.edu.au To: Hello, I'd appreciate if you could pass this on to anyone who may be interested. We're looking for a senior 7T Facility Fellow for our new Siemens 7 Tesla Whole Body MRI system to be installed later this year in Brisbane, Australia. Please see the full job details at: http://uqjobs.uq.edu.au/jobDetails.asp?sJobIDs=494467lCategoryID=lBrandID=lWorkTypeID=lLocationID=stp=AWsLanguage=en This is a great opportunity for someone to lead development of the new 7T MRI facility at the University of Queensland (and Brisbane is always sunny). -+- A/Prof Ross Cunnington, Principal Research Fellow Queensland Brain Institute School of Psychology University of Queensland, Brisbane, Australia Phone: +61 7 3346 6330 Begin forwarded message: From: Rebecca Osborne rebecca.osbo...@cai.uq.edu.aumailto:rebecca.osbo...@cai.uq.edu.au Subject: 7T Facility Fellow Position at CAI Date: 11 March 2013 9:10:33 AM AEST To: CAI_Staff cai_st...@exchange.uq.edu.aumailto:cai_st...@exchange.uq.edu.au Cc: Ross Cunnington r.cunning...@uq.edu.aumailto:r.cunning...@uq.edu.au, Stuart Crozier stu...@itee.uq.edu.aumailto:stu...@itee.uq.edu.au Hi All The advertisement for the 7T Facility Fellow position at CAI is now on UQ jobs. The position will be advertised internationally, however please feel free to circulate this link to any professional networks that you feel may be appropriate. http://uqjobs.uq.edu.au/jobDetails.asp?sJobIDs=494467lCategoryID=lBrandID=lWorkTypeID=lLocationID=stp=AWsLanguage=en thanks - Bec Rebecca Osborne Deputy Director, Operations Centre for Advanced Imaging The University of Queensland T: +61 7 3365 4235 rebecca.osbo...@cai.uq.edu.aumailto:rebecca.osbo...@cai.uq.edu.au ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_cvs_register - use of wmparc instead of aseg
Dear Lilla, i'm currently applying mri_cvs_register and I'm very happy with the nice results. Congratulation for this very clever approach. However, some data sets which I work on have still aseg.mgz which are not segmented appropriately. As far as I understand aseg.mgz is not redefined after e.g. pial-edits or added control points. Thus, I think it might be better to use aparc+aseg or wmparc instead of aseg within mri_cvs_register. Taking this into account I have the following questions: 1. Do you have experience with mri_cvs_register and --asegfname Option different from aseg? Does it impact the processing time? Are there options, which have to be adopted? 2. Since I think it is better to use aseg instead of wmparc, since it contains fewer IDs and registration will not be overfitted, is there a convenient way to generate a new aseg.mgz, which includes manual corrections like pial edits? 3. The last question regards the norm.mgz ... since it also often contains to much (outer brain) volume .. would it be better to mask norm.mgz with (e.g.) wmparc or a dilated version of wmparc before using it with mri_cvs_register ? Thanks you, Daniel Universitätsklinikum Jena - Bachstrasse 18 - D-07743 Jena Die gesetzlichen Pflichtangaben finden Sie unter http://www.uniklinikum-jena.de/Pflichtangaben.html ___ 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] convert from vtk to Freesurfer surface file format
Hello, I would like to use the surface registration tools in Freesurfer. I first need to convert my vtk surfaces into the Freesurfer format. I tried mris_convert, but this seems to only convert from and not to the Freesurfer file format. Does anyone know of another conversion tool available? Thanks for your help, Christine. ___ Christine L Tardif, PhD Postdoctoral fellow Max Planck Institute for Human Cognitive and Brain Sciences Department of Neurophysics www.cbs.mpg.de/~ctardif ___ 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] Stat doubts
Dear Freesurfers I'm performing regression analyses including confounding variables, and I would like to know how to obtain the following information:A) The squre Rand B) The standarized beta coefficient of an independient variable; and the partial correlation with its p-valuesMany thanks in advanced,Gabriel ___ 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] Stat doubts
Hi Gabriel, I've attached a matlab routine which will compute the PCC.
If you cd into the GLM dir, then
X = load('Xg.dat');
beta = MRIread('beta.mgh');
C = load('yourcontrast/C.dat');
rvar = MRIread('rvar.mgh');
betamat = fast_vol2mat(beta);
rvarmat = fast_vol2mat(rvar);
rhomat = fast_glm_pcc(betamat,X,C,rvarmat);
rho = beta;
rho.vol = fast_mat2vol(rhomat,rho.volsize);
MRIwrite(rho,'yourcontrast/pcc.mgh')
The R2 should just be the square of the PCC, right?
For the standardized beta, do you just divide the beta by sqrt(rvar)?
doug
On 3/14/13 1:39 PM, Gabriel Gonzalez Escamilla wrote:
Dear Freesurfers
I'm performing regression analyses including confounding variables,
and I would like to know how to obtain the following information:
A) The squre R
and
B) The standarized beta coefficient of an independient variable; and
the partial correlation with its p-values
Many thanks in advanced,
Gabriel
___
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function rho = fast_glm_pcc(beta,X,C,rvar)
% rho = fast_glm_pcc(beta,X,C,rvar)
%
% Computes the partial correlation coefficient of the given
% univariate contrast.
%
% WARNING: X must have a column of 1s or both X and y must have
% been demeaned before the glm.
%
% $Id: fast_glm_pcc.m,v 1.2 2012/11/19 22:18:23 greve Exp $
if(nargin ~= 4)
fprintf('rho = fast_glm_pcc(beta,X,C,rvar)\n');
return;
end
[J nbeta] = size(C);
if(J ~= 1)
fprintf('ERROR: fast_glm_pcc: contrast must be univariate\n');
return;
end
ntp = size(X,1);
DOF = ntp - nbeta;
% Design matrix projected onto the contrast space. This forms
% the space of the contrast
Xc = X*C';
% Null space of the contrast
D = null(C);
% Design matrix projected onto the null-space contrast. This forms
% the space of the nuisance regressors
Xd = X*D;
% Residual-forming matrix of the nuisance regressors
Rd = eye(ntp) - Xd*inv(Xd'*Xd)*Xd';
% Orthogonalize both Xc and yhat wrt the nuisance regressors
Xcd = Rd*Xc;
yhatd = Rd*(X*beta);
% Compute sums and cross-products needed for correlation coef
Xcdtyz = Xcd'*yhatd;
sumXcd = sum(Xcd);
sumyz = sum(yhatd); % Fails without column of 1s in X
XcdtXcd = sum(Xcd.^2);
yztyz = sum(yhatd.^2) + DOF*rvar;
rho = (Xcdtyz-sumXcd.*sumyz)./sqrt((XcdtXcd-sumXcd.^2).*(yztyz-sumyz.^2));
return;
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[Freesurfer] Permission denied
Dear FS team, I dowloaded the latest ML version of FS and tried to run a subject.But this error is coming up.Any suggestions? chikkuvarghese$ recon-all -i /Users/chikkuvarghese/Desktop/BL/raw/image1 -autorecon-all -s BL1 mkdir: /Applications/freesurfer/subjects/BL1: Permission denied mkdir: /Applications/freesurfer/subjects/BL1/scripts: Permission denied mkdir: /Applications/freesurfer/subjects/BL1/scripts: Permission denied cp: /Applications/freesurfer/subjects/BL1/scripts/build-stamp.txt: No such file or directory cat: /Applications/freesurfer/subjects/BL1/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer /Applications/freesurfer/subjects/BL1: No such file or directory. chikkus-MacBook-Pro:~ chikkuvarghese$ ___ 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] Permission denied
you probably want to specify the SUBJECTS_DIR as being somewhere else that you have write permission to. You can do this with the -sd path on the recon-all command line, or in the environment. cheers Bruce On Thu, 14 Mar 2013, Varghese Chikku wrote: Dear FS team,I dowloaded the latest ML version of FS and tried to run a subject.But this error is coming up.Any suggestions? chikkuvarghese$ recon-all -i /Users/chikkuvarghese/Desktop/BL/raw/image1 -autorecon-all -s BL1 mkdir: /Applications/freesurfer/subjects/BL1: Permission denied mkdir: /Applications/freesurfer/subjects/BL1/scripts: Permission denied mkdir: /Applications/freesurfer/subjects/BL1/scripts: Permission denied cp: /Applications/freesurfer/subjects/BL1/scripts/build-stamp.txt: No such file or directory cat: /Applications/freesurfer/subjects/BL1/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer /Applications/freesurfer/subjects/BL1: No such file or directory. chikkus-MacBook-Pro:~ chikkuvarghese$ ___ 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] Coordinates of center of gravity of a cluster in Freesurfer
Hi all, I would like to calculate the coordinates of center of gravity of a cluster in Freesurfer. Is there a way to do this in Freesurfer? Thanks, Nasim ___ 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] Estimate of number of manual edits and time to complete in 100subject sample
Hi Kev, For the two scenarios you mentioned, here are my best estimates. I assume a healthy, adult population scanned with our recommended sequences. Any other type of dataset (pediatric, one with some type of pathology, one acquired long ago using a less than optimal sequence or coil, etc.) would likely differ by a lot in terms of time estimates. 1. fMRI on good quality 3T Maybe 25 out of 100 need some kind of intervention, including restarting a process that may have failed along the way. I would expect these 25 to have something terribly wrong with them to make them unacceptable for fMRI analysis but something that is most likely easily fixed by an automatic intervention. I'd estimate a half hour for each of the 25 or an hour for each to be extremely conservative. 2. Cortical thickness on good quality 3T Maybe 50-75 out of 100 need some kind of intervention, depending on which areas you might focus on if you're not only interested in global thickness. Edits on half of those will be very small, 15-30 minutes a case. Edits on the other half may be more time consuming, 30 minutes to 1 hour. Allison On Tue, 5 Mar 2013, Schumman Resonance wrote: This is a question for the FS community in general, I gather there is variability around this, but rather than an exact number and time, I was hoping for an estimate on how many scans would I expect to require manual edits(any of the check points recommended in the tutorials) as well as an estimate of the time it takes to go through them. For the sake of the argument, take a sample of 100 subjects. Thanks, Kev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] long_qdec_table
Hi Chris, the cross qdec table is messed up ( a single line without line breaks). long_qdec_table has problems reading your long-table because it contains 'tabs', several spaces instead of a single one between other columns and also not the line breaks it expects (the windows format). I will look into this, to see if I can make the program more flexible with respect to the input. In the meantime, you can - replace tabs with spaces - replace multiple spaces with single space - replace line breaks with linux style line breaks open it in linux with nedit and you'll see. Best, Martin On 03/13/2013 08:20 AM, Christopher McCarthy wrote: Hey All, I am trying to turn my long.qdec.table.dat into a cross.qdec.table.dat using the following command: long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat However, when I try and load it into QDEC afterwards I get the following error: Loading data table /data/freesurfer/qdec/cross.qdec.table.dat... Number of columns: 103 fsid column:1 Number of factors: 102 Number of subjects: 0 ERROR: QdecDataTable::Load: number of subjects = 0 Error loading the data table. I attached both the long.qdec and the cross.qdec tables, if someone knows what I am doing wrong, I would love some help! Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] long_qdec_table
Hi Chris, try to rename the LongQdecTable.* files in your FS install and place a new LongQdecTable.py file there from here: http://martinos.org/~mreuter/LongQdecTable.py the new one uses universal newline support. Not sure if the Python on your system supports this. Let me know (also what system you are using and what OS version, also the version of Python) Thanks, Martin On 03/13/2013 08:20 AM, Christopher McCarthy wrote: Hey All, I am trying to turn my long.qdec.table.dat into a cross.qdec.table.dat using the following command: long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat However, when I try and load it into QDEC afterwards I get the following error: Loading data table /data/freesurfer/qdec/cross.qdec.table.dat... Number of columns: 103 fsid column:1 Number of factors: 102 Number of subjects: 0 ERROR: QdecDataTable::Load: number of subjects = 0 Error loading the data table. I attached both the long.qdec and the cross.qdec tables, if someone knows what I am doing wrong, I would love some help! Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] volumetrics questions
Hello experts, I am doing volumetric studies where I am comparing the subcortical structures volumes among different experimental groups. I usually do two mprages on one subject in a single scan at two time-points. I run recon all on both mprages for a single subjects. To my surprise the volumes of same structure of a single subject calculated by freesurfer using two mprages are different. I did longitudinal run using the two mprages from same subject, however then also the volumes show differences. May you please advise me what to do. Thanks, Rashmi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] volumetrics questions
Hi Rashmi of course they are different - there is noise in the scans and motion and other sources of corruption! The amount of difference will depend on the structure and the quality of the data. cheers Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote: Hello experts, I am doing volumetric studies where I am comparing the subcortical structures volumes among different experimental groups. I usually do two mprages on one subject in a single scan at two time-points. I run recon all on both mprages for a single subjects. To my surprise the volumes of same structure of a single subject calculated by freesurfer using two mprages are different. I did longitudinal run using the two mprages from same subject, however then also the volumes show differences. May you please advise me what to do. Thanks, Rashmi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] volumetrics questions
Thank you Bruce. So what should I do. Shall I just take one of the mprage values or is it a good idea to get the average from two mprages for each structure. Can longitudinal run be helpful? Please suggest. Thank you! Rashmi On 3/14/13 12:09 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Rashmi of course they are different - there is noise in the scans and motion and other sources of corruption! The amount of difference will depend on the structure and the quality of the data. cheers Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote: Hello experts, I am doing volumetric studies where I am comparing the subcortical structures volumes among different experimental groups. I usually do two mprages on one subject in a single scan at two time-points. I run recon all on both mprages for a single subjects. To my surprise the volumes of same structure of a single subject calculated by freesurfer using two mprages are different. I did longitudinal run using the two mprages from same subject, however then also the volumes show differences. May you please advise me what to do. Thanks, Rashmi The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] volumetrics questions
yes, you should use the longitudinal stream for your analysis. You are probably better off picking the better mprage (i.e. less motion) and analyzing it at each timepoint cheers Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote: Thank you Bruce. So what should I do. Shall I just take one of the mprage values or is it a good idea to get the average from two mprages for each structure. Can longitudinal run be helpful? Please suggest. Thank you! Rashmi On 3/14/13 12:09 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Rashmi of course they are different - there is noise in the scans and motion and other sources of corruption! The amount of difference will depend on the structure and the quality of the data. cheers Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote: Hello experts, I am doing volumetric studies where I am comparing the subcortical structures volumes among different experimental groups. I usually do two mprages on one subject in a single scan at two time-points. I run recon all on both mprages for a single subjects. To my surprise the volumes of same structure of a single subject calculated by freesurfer using two mprages are different. I did longitudinal run using the two mprages from same subject, however then also the volumes show differences. May you please advise me what to do. Thanks, Rashmi The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] volumetrics questions
Ok I have done that. I did run longitudinal run using each mprage as an individual timepoint. So this way I got the longitudinal run stat output for both time points. So do you suggest I average them out or take the result of the output from one of the long run. Or are you suggesting that I take the volumes from the base run output. This seems so simple, am I complicating it? Sorry if I am not understanding you! Please advise. Rashmi On 3/14/13 12:15 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: yes, you should use the longitudinal stream for your analysis. You are probably better off picking the better mprage (i.e. less motion) and analyzing it at each timepoint cheers Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote: Thank you Bruce. So what should I do. Shall I just take one of the mprage values or is it a good idea to get the average from two mprages for each structure. Can longitudinal run be helpful? Please suggest. Thank you! Rashmi On 3/14/13 12:09 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Rashmi of course they are different - there is noise in the scans and motion and other sources of corruption! The amount of difference will depend on the structure and the quality of the data. cheers Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote: Hello experts, I am doing volumetric studies where I am comparing the subcortical structures volumes among different experimental groups. I usually do two mprages on one subject in a single scan at two time-points. I run recon all on both mprages for a single subjects. To my surprise the volumes of same structure of a single subject calculated by freesurfer using two mprages are different. I did longitudinal run using the two mprages from same subject, however then also the volumes show differences. May you please advise me what to do. Thanks, Rashmi 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] question about autorecon2-cp, autorecon-pial and autorecon-wm flags
Hi Folks, I was looking at the autorecon2-cp, autorecon-pial and autorecon-wm flags in recon-all help and also here http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags My interpretation is when I use autorecon-pial, I only need the command: recon-all --autorecon-pial -s subject While for autorecon2-cp and autorecon2-wm we need the command: recon-all -autorecon2-cp -autorecon3 -s subject recon-all -autorecon2-wm -autorecon3 -s subject since for autorecon2-cp and autorecon2-wm only a subset of stages are processed as described in recon-all help: -autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ mri_seg) -autorecon2-wm : process stages 15-23 Thanks Mehul ___ 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] volumetrics questions
what is your goal? If it is to detect longitidinal change I would advise take the best mprage at each timepoint and run it through cross-sectional then longitudinal analysis Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote: Ok I have done that. I did run longitudinal run using each mprage as an individual timepoint. So this way I got the longitudinal run stat output for both time points. So do you suggest I average them out or take the result of the output from one of the long run. Or are you suggesting that I take the volumes from the base run output. This seems so simple, am I complicating it? Sorry if I am not understanding you! Please advise. Rashmi On 3/14/13 12:15 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: yes, you should use the longitudinal stream for your analysis. You are probably better off picking the better mprage (i.e. less motion) and analyzing it at each timepoint cheers Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote: Thank you Bruce. So what should I do. Shall I just take one of the mprage values or is it a good idea to get the average from two mprages for each structure. Can longitudinal run be helpful? Please suggest. Thank you! Rashmi On 3/14/13 12:09 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Rashmi of course they are different - there is noise in the scans and motion and other sources of corruption! The amount of difference will depend on the structure and the quality of the data. cheers Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote: Hello experts, I am doing volumetric studies where I am comparing the subcortical structures volumes among different experimental groups. I usually do two mprages on one subject in a single scan at two time-points. I run recon all on both mprages for a single subjects. To my surprise the volumes of same structure of a single subject calculated by freesurfer using two mprages are different. I did longitudinal run using the two mprages from same subject, however then also the volumes show differences. May you please advise me what to do. Thanks, Rashmi The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Xhemi files do not exist in the specified ftp location
Dear Doug,
Following up on my yesterday email, I would appreciate if you kindly upload
the following files (required for Xhemi) so the ftp download will be
possible. I am currently using version 5.1 of FreeSurfer and need the
installation of these files in order to be able to run the Xhemi process.
Thank you.
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemireg
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.tar.gz
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mult-comp-cor.tar.gz
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.{linux,mac}
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol.{linux,mac}
Regards,
Negar
On Wed, Mar 13, 2013 at 2:50 PM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote:
Oh, sorry, those get periodically deleted. Are you using 5.2? If so they
are already in the distribution. If not, I'll copy them back over.
doug
On 3/13/13 10:33 PM, Negar Memarian wrote:
Dear Doug,
Can you please advise me of the correct location of the ftp
directories/files required to be installed for surface based
interhemispheric registration?
I'm trying to download and install the required files from the specified
path:
ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/but
the files/folders (e.g., surfreg, mris_preproc , fsaverage_sym.tar.gz ,
etc) do not exist.
I appreciate your help.
Regards,
Negar
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
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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] Process flow: ReconAllDevTable
Hi Nick I have a followup question about Scenario D: Scenario D (for pial edits): 1. recon-all -s subject -autorecon1 -autorecon2 2. edit brainmask.mgz ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits) 3. recon-all -s subject -autorecon-pial I think -autorecon-pial is a subset of -autorecon3 ? Is so then could i still run -autorecon-pial without running -autorecon3? Or if i did this would i miss some of the outputs generated by -autorecon3. Also if -autorecon-pial is a subset of autorecon3, is the following scenario valid. Scenario E (for pial edits): 1. recon-all -s subject -autorecon1 -autorecon2 2. edit brainmask.mgz ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits) 3. recon-all -s subject *-autorecon3 (instead of -autorecon-pial)* Thanks Mehul On Wed, Mar 13, 2013 at 12:31 PM, Mehul Sampat mpsam...@gmail.com wrote: Hi Nick, Thank you very much. I have two followup questions. Since Scenario B is permissible, I believe the following two scenarios should also be allowed. (Just wanted to confirm this:) Scenario C (for white matter edits): 1. recon-all -s subject -autorecon1 -autorecon2 2. edit wm.mgz ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits) 3. recon-all -s subject -autorecon2-wm -autorecon3 Scenario D (for pial edits): 1. recon-all -s subject -autorecon1 -autorecon2 2. edit brainmask.mgz ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits) 3. recon-all -s subject -autorecon2-pial Basically, I am trying to see if I can avoid running -autorecon3 in the first run; make all the edits and then re-run recon-all with appropriate flags. Thanks Mehul On Wed, Mar 13, 2013 at 10:58 AM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Mehul, Scenerio B is permissible. And to address your question, the pial surface is created in the autorecon3 stage, making use of the parcellation data to refine it. I think a pial is generated during make_final_surfaces as its normal output, but its overwritten in autorecon3. Nick On Wed, 2013-03-13 at 10:52 -0700, Mehul Sampat wrote: ps: just wanted to add a clarification to my question. The two scenarios are: Scenario A: 1. recon-all -s subject -autorecon1 -autorecon2 -autorecon3 2. add control points 3. recon -all -s subject -autorecon2-cp -autorecon3 Scenario B: 1. recon-all -s subject -autorecon1 -autorecon2 2. add control points 3. recon -all -s subject -autorecon2-cp -autorecon3 If Scenario B is permissible, the advantage is that, -autorecon3 is only run once thus saving a few hours of computation. Thanks Mehul On Wed, Mar 13, 2013 at 10:35 AM, Mehul Sampat mpsam...@gmail.com wrote: Hi Folks, Based on the tutorials, we normally run full recon-all pipeline; then add control points if required and then run -autorecon2-cp and -autorecon3 again. Recently, I was looking at the process flow table: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable and I have two questions: 1. From this table it seems like ?h.white is created in autorecon2 and ?h.pial is created in autorecon3. However, when i run recon-all -s subj -autorecon1 -autorecon2 i see that ?h.pial is also already created. Does this mean I am interpreting the process flow table incorrectly or is there an error in the table ? 2. Also if ?h.pial and ?h.white are already created at the end of autorecon2; then can we add control points at immediately after autorecon2 ? This way we would need to run autorecon3 only once and save resources. Or am I missing something and is it that one must run -autorecon2 and -autorecon3 and then add control points and then run -autorecon2-cp and -autorecon3 again. Thanks Mehul ___ 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
[Freesurfer] Caret to Freesurfer
I am new to Freesurfer, and I am trying to input/process preterm infant brain data (ultimately attempting longitudinal registration). I already have surfaces generated from Caret, as well as the original T1/T2 images. My question is: Does anything exist to take processed data from Caret into Freesurfer? If not, is there a good way to process the T1/T2 images in Freesurfer despite the differences in contrast and intensity (and anatomy)? Thank you in advance for your advice, Kara ___ 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 files do not exist in the specified ftp location
It is actually there. I changed the location but did not update the
wiki. Look in this dir
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfregxhemi-reg
On 3/14/13 7:43 PM, Negar Memarian wrote:
Dear Doug,
Following up on my yesterday email, I would appreciate if you kindly
upload the following files (required for Xhemi) so the ftp download
will be possible. I am currently using version 5.1 of FreeSurfer and
need the installation of these files in order to be able to run the
Xhemi process. Thank you.
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemireg
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.tar.gz
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mult-comp-cor.tar.gz
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.{linux,mac}
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.%7Blinux,mac%7D
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol.{linux,mac}
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol.%7Blinux,mac%7D
Regards,
Negar
On Wed, Mar 13, 2013 at 2:50 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
Oh, sorry, those get periodically deleted. Are you using 5.2? If
so they are already in the distribution. If not, I'll copy them
back over.
doug
On 3/13/13 10:33 PM, Negar Memarian wrote:
Dear Doug,
Can you please advise me of the correct location of the ftp
directories/files required to be installed for surface based
interhemispheric registration?
I'm trying to download and install the required files from the
specified path:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
but the files/folders (e.g., surfreg, mris_preproc ,
fsaverage_sym.tar.gz , etc) do not exist.
I appreciate your help.
Regards,
Negar
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
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: [Freesurfer] mri_cvs_register - use of wmparc instead of aseg
Hi Daniel. i'm currently applying mri_cvs_register and I'm very happy with the nice results. Congratulation for this very clever approach. However, some data sets which I work on have still aseg.mgz which are not segmented appropriately. As far as I understand aseg.mgz is not redefined after e.g. pial-edits or added control points. Thus, I think it might be better to use aparc+aseg or wmparc instead of aseg within mri_cvs_register. Taking this into account I have the following questions: 1. Do you have experience with mri_cvs_register and --asegfname Option different from aseg? Does it impact the processing time? Are there options, which have to be adopted? I only minimally experimented with this option, alowing users to use segmentation files that are edited or modified from the default version. processing time and registration options might change with a new file, but that will depend on thenature of the new file that you want to use. I belive that if you use either of the files that you mentioned above neither of those will (need to) change. 2. Since I think it is better to use aseg instead of wmparc, since it contains fewer IDs and registration will not be overfitted, is there a convenient way to generate a new aseg.mgz, which includes manual corrections like pial edits? If you make manual edits to the aseg.mgz file you can always save it under a different name and use the --asegfname option to indictae the new input to mri_cvs_register. For manual editing we recommend using Freeview and on the below page you may find useful advice http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewSegmentations 3. The last question regards the norm.mgz ... since it also often contains to much (outer brain) volume .. would it be better to mask norm.mgz with (e.g.) wmparc or a dilated version of wmparc before using it with mri_cvs_register ? That never caused a problem for me, and the answer in your case will depend on the amount of error that exists in your datasets. If you do decide to use a mask though, you should do that consistently on all of your data sets. Let me know if you have any further questions. Lilla ___ 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] Error messages and empty surf files
Hi Hayley the LINE SEARCH messages can be ignored, but not the watershed one. The watershed error means the skull stripping has failed, possibly because of a talairach normalization problem. Have you checked the talairach.xfm and the brain.mgz? That's where I would start cheers Bruce On Thu, 14 Mar 2013, Hayley Dorfman wrote: Hello, I'm having trouble with recon-all. For 1 of 49 subjects, it completes with the following error: mri_watershed Error: GLOBAL region of the brain empty ! Other errors are found in the log which read: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCES This subject's surf files are also empty. I found this thread from two years ago mentioning a similar issue, but a solution was not available: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18863.html Has there been any progress? I've attached my log file. Any help is much appreciated! -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] Caret to Freesurfer
Hi Kara I think the answer is yes as there are people at Wash U that do this routinely. Maybe Matt Glasser or someone else can chime in? cheers Bruce On Thu, 14 Mar 2013, Ellspermann, Kara wrote: I am new to Freesurfer, and I am trying to input/process preterm infant brain data (ultimately attempting longitudinal registration). I already have surfaces generated from Caret, as well as the original T1/T2 images. My question is: Does anything exist to take processed data from Caret into Freesurfer? If not, is there a good way to process the T1/T2 images in Freesurfer despite the differences in contrast and intensity (and anatomy)? Thank you in advance for your advice, Kara ___ 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] Caret to Freesurfer
She wants to go from Caret to FreeSurfer, rather than from FreeSurfer to Caret, which is what I do. Kara, I believe we are meeting tomorrow to discuss the options for this? I don't know anything about the FreeSurfer longitudinal pipeline, but it would take going through the pipeline and finding all of the inputs needed and converting them or generating them. I think the main goal here is to use the longitudinal surface registration. Matt. On 3/14/13 8:04 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kara I think the answer is yes as there are people at Wash U that do this routinely. Maybe Matt Glasser or someone else can chime in? cheers Bruce On Thu, 14 Mar 2013, Ellspermann, Kara wrote: I am new to Freesurfer, and I am trying to input/process preterm infant brain data (ultimately attempting longitudinal registration). I already have surfaces generated from Caret, as well as the original T1/T2 images. My question is: Does anything exist to take processed data from Caret into Freesurfer? If not, is there a good way to process the T1/T2 images in Freesurfer despite the differences in contrast and intensity (and anatomy)? Thank you in advance for your advice, Kara ___ 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] mri_convert problem
Hi, I have a problem of conversion. I would like to convert mnc file to mgz. But I think I shoul first convert mnc to nii then nii to mgz. , so I try the command mri_convert and I have this error; -[esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc Folder1.nii.gzmri_convert /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc Folder1.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $reading from /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc...mincRead(): can't find file /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc[esther@m3012-04 ~]$ I look up, and the file is at the rith place Could you help me..Thanks VP] ___ 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.
