Freesurfer February 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
236 discussions

Re: [Freesurfer] extracting hand drawn ROIs to Afni space
by Douglas N Greve 27 Feb '13

27 Feb '13

You can load the segmentation as both a segmentation and an input volume in tkmedit, eg tkmedit subject orig.mgz -aux gmroi_volume.nii.gz -seg gmroi_volume.nii.gz You can then see the number of each of your segmentations in the Aux field when you click on your segmentation. There's probably an easier way, but I can't remember the series of commands you ran to get gmroi. Send them if you want a better way. doug On 02/27/2013 04:21 PM, Paul Beach wrote: > Well, what I've been doing is using a 3dcalc command to call forth > regions that are part of the segmented parcellations of each subject. > These, of course, are regions that are found in the LUT. The 3dcalc > command calls them forth by using their LUT number. > > For example, when in a given subject's Afni folder, I can use this > command: > 3dcalc -a gmroi_volume.nii.gz -expr 'equals(a,1026)' -prefix > ROI_FS_lh.rACC.nii.gz > > It then gives me, in Afni space, the rostral anterior cingulate on > that subject's brain. I can then run my normal correlation analysis > scripts on this region. > > However, for the regions that I added into the automatic > parcellations/segmentation (through your help) I don't have a number > to call them forward as they are not in the LUT. SO, I'm left with the > question as to whether there is another way to get them out of the > aparc.aseg file that doesn't require me to make a new LUT > (i.e.appending the new regions into it). If there isn't a way, then > how does one go about making changes to the LUT and getting Freesurfer > to then associate those changes with the aparc.aseg file. > > > Hopefully that all made sense. > > > Paul > > > > On Tue, Feb 26, 2013 at 5:41 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Paul, I'm not sure I understand. What does 3dcalc have to do > with the LUT? > doug > > > On 02/25/2013 05:13 PM, Paul Beach wrote: > > Hi Doug. Thank you for the e-mail. > > I do, actually, have a 'next step' problem. > > I've been able to get ROIs drawn in tksurfer into an augmented > aparc+aseg file of an averaged subject. Now I need to be able > to get those ROIs, which are not part of the color LUT, into > Afni space. > > For ROIs that are already in the LUT, getting them to Afni is > no problem, I simply use a 3dcalc command that utilizes their > place in the LUT. However, I have the problem of needing to > export the newly parcellated and segmented ROIs that aren't in > the Freesurfer LUT to Afni space. > > Is there a way to do this short of creating a new "spot" for > them in our LUT? If not, how does one go about adding ROIs to > the LUT and/or creating a LUT specific to my needs (since the > Wiki suggests not fussing with the original LUT)? > > > Thanks, > Paul > > > > On Mon, Feb 25, 2013 at 11:28 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Hi Paul, do you still have a problem that needs to be solved? > doug > > > On 02/18/2013 04:39 PM, Paul Beach wrote: > > Thank you for forwarding this. > > > > I realize I need to further clarify my issue as well. > > > > With the help of Doug Greve I've taken hand made ROIs in > tksurfer, > > repackaged them into a new annotation, and repackaged > that into > a new > > aseg file for an average subject. Now (and this is where > I'm stuck) > > I'm trying to take those newly minted ROIs, place them onto > individual > > subjects' brains and THEN send them to Afni for each of > those > subjects > > (before doing seed correlation analysis). > > > > Previously I had been using mri_label2label to place the > averaged > > subject ROI into single subjects' folders and then > mri_label2vol to > > get them ready to send to Afni. However, this method was not > producing > > ROIs that covered the extent of a region's gray matter. > Thus, Doug's > > solution of re-annotating and re-segmenting. > > > > Hopefully that makes things a bit easier. > > > > > > Thanks again for your help! > > Paul > > > > > > On Mon, Feb 18, 2013 at 3:13 PM, Bruce Fischl > > <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>> wrote: > > > > Hi Paul > > > > we usually call those labels and have an ascii label > file > format. > > Not sure how to get that into AFNI, but I'm zure > Ziad (ccd) > knows. > > > > cheers > > Bruce > > > > On Mon, 18 Feb 2013, Paul Beach wrote: > > > > Hi there, > > Through the help of the Freesurfer Q&A staff > I've been > able to > > get ROIs > > drawn in tksurfer into an augmented aparc+aseg > file of an > > averaged subject. > > I need to be able to get those ROIs, which are > not part > of the > > color LUT, > > into Afni space. > > > > For ROIs that are already in the LUT, getting > them to > Afni is > > no problem, I > > simply use a 3dcalc command. However, I have the > problem of > > needing to > > export newly parcellated and segmented ROIs that > aren't > in the > > Freesurfer > > LUT to Afni space. > > > > Is there a way to do this short of creating a > new "spot" for > > them in our > > LUT? If not, how does one go about adding ROIs > to the LUT > > and/or creating a > > LUT specific to my needs (since the Wiki > suggests not > fussing > > with the > > original LUT)? > > > > > > Thanks, > > Paul > > -- > > > > > > > > > > > > The information in this e-mail is intended only for the > person to > > whom it is > > addressed. If you believe this e-mail was sent to you in > error and > > the e-mail > > contains patient information, please contact the > Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail > was sent to > > you in error > > but does not contain patient information, please > contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > -- > > Paul Beach > > DO/PhD candidate - Year V > > Michigan State University > > - College of Osteopathic Medicine - OMS V > > - Neuroscience Program > > - Bozoki Lab: Neurology/Radiology > > - President: American Physician Scientist Association, > MSU COM > Chapter > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > Paul Beach > DO/PhD candidate - Year V > Michigan State University > - College of Osteopathic Medicine - OMS V > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology > - President: American Physician Scientist Association, MSU COM > Chapter > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > -- > Paul Beach > DO/PhD candidate - Year V > Michigan State University > - College of Osteopathic Medicine - OMS V > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology > - President: American Physician Scientist Association, MSU COM Chapter -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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/

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LGI Path Question
by Adam David Felton 27 Feb '13

27 Feb '13

Hello, I'm trying to run LGI. We have the 2012 version of matlab and the image processing toolbox. I've looked at several threads dealing with path issues, but have been unable to fix my problem. I think our problem is that when I run "recon-all -s ucr001_4-11 -localGI" it seems to start up properly, but then it's calling Matlab 2010 instead of 2012. Here's the error message we get: ====================================================== Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2010 The MathWorks, Inc. Version 7.10.0.499 (R2010a) 64-bit (maci64) February 5, 2010 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> ??? Undefined function or method 'make_outer_surface' for input arguments of type 'char'. >> ERROR: make_outer_surface did not create output file '/Users/Tiana/ucr_freesurfer_data/subjects_10/ucr001_4-11/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Darwin bryden.ucr.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 ====================================================== Then I moved Matlab2010 to see if it would load Matlab2012 and I got this error: ====================================================== bryden:~ Tiana$ recon-all -s ucr001_4-11 -localGI Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /Users/Tiana/ucr_freesurfer_data/subjects_10 Actual FREESURFER_HOME /Applications/freesurfer -rw-r--r-- 1 Tiana staff 1839026 Feb 27 10:34 /Users/Tiana/ucr_freesurfer_data/subjects_10/ucr001_4-11/scripts/recon-all.log Darwin bryden.ucr.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 /Users/Tiana/ucr_freesurfer_data/subjects_10/ucr001_4-11/surf #-------------------------------------------- #@# Local Gyrification Index lh Wed Feb 27 10:41:59 PST 2013 \n mris_compute_lgi --i lh.pial \n ERROR: Matlab is required to run mris_compute_lgi! Darwin bryden.ucr.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 recon-all -s ucr001_4-11 exited with ERRORS at Wed Feb 27 10:41:59 PST 2013 ====================================================== I have been unable to find out how to have FreeSurfer call Matlab 2012. My startup.h file looks like this now: %------------ FreeSurfer -----------------------------% fshome = getenv('FREESURFER_HOME'); $FREESURFER_HOME/matlab; fsmatlab = sprintf('/Users/Tiana/matlab',fshome); path(path,fsmatlab); clear fshome fsmatlab; %-----------------------------------------------------% I used the full code for startup.m given by Nick and others but then Matlab2012 didn't open up properly; with this code Matlab2012 opens up without errors. Is there a place in Freesurfer to define the path for Matlab? Any help would be greatly appreciated. Thank you, Adam

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Qdec
by Varghese Chikku 27 Feb '13

27 Feb '13

Dear all, I am bit confused with the Qdec process. I finished recon all for 2 time points and want to create longitudinal data.From FS tutorial I learned to create within-subject templates for processing,which is running now with recon-all -base <templateID> -tp <tp1id> -tp <tp2id> ... -all. Now,in an other link of tutorial it says ,Qdec needs each subject to have a pre-computed smoothed data for the target surface ,recon-all -s <subjid> -qcache So my first is question is, recon-all -base <templateID> -tp <tp1id> -tp <tp2id> ... -all will do recon-all -s <subjid> -qcache along or I have to run it separately. Second,recon-all -base <templateID> -tp <tp1id> -tp <tp2id> ... -all is almost 12 hrs now and wondering if this is processing images from the very begining. Many Thanks chikku

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surface based analyses using PET
by Léorah Freeman 27 Feb '13

27 Feb '13

Dear FreeSurfers, I would like to perform surface based analyses using PET but I am not sure I am doing things correctly. For each subject, I have reconstructed the 3DT1 MRI using recon-all –all. Then I have coregistered the PETs with the anatomical using: Bbregister --s name --mov pet.nii --bold --init-fsl --reg pet_2_T1_register.dat Registration worked very well. Now I am trying to process the PET in order to do a surface based analysis of the PET signal. I was thinking of running: 1) mris_preproc --target fsaverage --hemi lh --iv subject1/pet/subject1_pet.nii subject1/pet/pet_2_T1_register.dat --iv subject2/pet/subject2_pet.nii subject2/pet/pet_2_T1_register.dat --iv subject3/pet/subject3_pet.nii subject3/pet/pet_2_T1_register.dat (…) --projfrac 0.5 --out lh.pet.mgh I am not sure this is the right command line. I am especially concerned with the registration file I should use. Here I used the PET àMRI registration file. Is this the right one to use. Or should I use a registration file from native space to fsaverage space. If so, how do I do that? 2) mri_surf2surf --hemi lh --s fsaverage --fwhm 10 --cortex --sval lh.pet.mgh --tval lh.pet.sm10.mgh Any advice on the fwhm I should use for smoothing the data to the surface? 3) mri_glmfit --y lh.fmz.sm10.mgh --fsgd fsgd.txt --C X.mtx --surf fsaverage lh --cortex --glmdir lh.pet-age.glmdir Can you please tell me if I got it right, especially regarding the registration file I should use with mris_preproc? Thank you so much, Leorah Freeman, MD, MSc

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Re: [Freesurfer] Problem with glmfit: matrix is ill-conditioned
by Ed Gronenschild 27 Feb '13

27 Feb '13

Hi Doug, Can I do this by just permuting the contrast matrix and the corresponding columns in the fsgd file? Ed On 26 Feb 2013, at 17:43, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Hi Ed, I think it is just the way you have the matrix set up. You'll need to alter the matrix in some way. doug > Message: 7 > Date: Tue, 26 Feb 2013 10:08:07 +0100 > From: Ed Gronenschild <ed.gronenschild(a)maastrichtuniversity.nl> > Subject: Re: [Freesurfer] Problem with glmfit: matrix is > ill-conditioned > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <2031202F-E366-48CB-82A9-3142378AD2FF(a)maastrichtuniversity.nl> > Content-Type: text/plain; charset="us-ascii" > > Hi Doug, > > The condition numbers were: > - 1e+08 for problematic fsgd file > - 371.233 for previous fsgd file > > I tried also v5.1, however with no succes. The matirx was still > ill-conditioned with condition number 2.80809e+07. > > Cheers, > Ed > > On 1 Feb 2013, at 9:53, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > >> Message: 12 >> Date: Thu, 31 Jan 2013 14:08:11 -0500 >> From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] Problem with glmfit: matrix is >> ill-conditioned >> To: freesurfer(a)nmr.mgh.harvard.edu >> Message-ID: <510AC11B.4090902(a)nmr.mgh.harvard.edu> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> >> Hi Ed, that sounds strange. What were the condition numbers for the >> two >> analyses? This should be printed out into the terminal. It is also >> possible that it is a scaling issue. This should not be an issue in >> 5.1, >> but it is possible that it could have an effect if two columns are >> very >> similar. >> doug >> >> >> On 01/30/2013 05:10 AM, Ed Gronenschild wrote: >>> >>> Hi Doug, >>> >>> It is indeed correct that columns 1 and 17 are highly correlated. >>> However, >>> for another version of the fsgd file, where the corresponding >>> class and >>> covariate values where identical but with other covariates (so >>> leading to >>> the same columns 1 and 17, other columns are different), all went >>> well. >>> So probably some other columns are highly correlated as well. >>> Anyway, what can we do about it? Just leave the offending covariate >>> (s) >>> out? >>> >>> Cheers, >>> Ed >>> >>> >>> >>>> Message: 1 >>>> Date: Thu, 24 Jan 2013 12:51:23 -0500 >>>> From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu >>>> <mailto:greve@nmr.mgh.harvard.edu>> >>>> Subject: Re: [Freesurfer] Problem with glmfit: matrix is >>>> ill-conditioned >>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>>> Message-ID: <5101749B.4060305(a)nmr.mgh.harvard.edu >>>> <mailto:5101749B.4060305@nmr.mgh.harvard.edu>> >>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>>> >>>> Hi Ed, the problem is that your covariates are highly correlated. >>>> Eg, >>>> column 1 is nearly identical to column 17. >>>> doug >>>> >>>> >>>> On 01/24/2013 06:36 AM, Ed Gronenschild wrote: >>>>> Hi, >>>>> >>>>> Running mri_glmfit ( v5.0.0, Mac OSX10.6) I got he following >>>>> error message: >>>>> >>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 >>>>> Possible problem with experimental design: >>>>> Check for duplicate entries and/or lack of range of >>>>> continuous variables within a class. >>>>> If you seek help with this problem, make sure to send: >>>>> 1. Your command line: >>>>> mri_glmfit --y lh.sib_con_cann_aangepast3.thickness.sm0.mgh >>>>> --fsgd >>>>> ../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/ >>>>> fsgd_sib_con_cann_aangepast3.fsgd >>>>> dods --glmdir lh.sib_con_cann_aangepast3.dods.sm0.glmdir --surf >>>>> fsaverage lh --C >>>>> ../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/ >>>>> group_thickness_gender_scan_age_educ_hand_cann.mtx >>>>> >>>>> 2. The FSGD file (if using one) >>>>> 3. And the design matrix above >>>>> >>>>> Please find attached the requested files. >>>>> >>>>> I noticed that rows 68 and 147 of the matrix Xg.dat are identical, >>>>> and most probably caused the error. >>>>> In the fsgd file I see that the correspondig cases indeed have >>>>> identical values, although they are referring to different data. >>>>> How to proceed? >>>>> >>>>> Cheers, >>>>> Ed >>>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)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/ > >

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Postdoctoral Position Boston Children's Hospital/Harvard Medical School
by Gaab, Nadine 27 Feb '13

27 Feb '13

The Gaab Lab http://www.childrenshospital.org/research/gaablab and (www.babymri.org)<http://www.babymri.org)>) at the Laboratories of Cognitive Neuroscience at Children's Hospital Boston (Developmental Medicine Center) invites applications for a NIH funded post-doctoral associate in the area of developmental cognitive neuroscience/pediatric fMRI. Available resources include a 3.0T MRI scanner, a child-friendly Mock scanner and analysis platforms based in MATLAB/UNIX. The candidate will be expected to design, organize and conduct pediatric and infant (f)MRI experiments, analyze behavioral and fMRI data, prepare manuscripts for publication, and participate in conferences. The NIH and foundation funded projects will focus on neural and behavioral pre-markers of developmental dyslexia in infants and pre-reading children as well as typical reading and language development. The successful applicant should have a doctoral degree in a field related to developmental cognitive neuroscience (e.g., cognitive neuroscience, neuroscience, developmental psychology, medicine or psychology). Individuals with a background in electrical engineering, biomedical engineering or computer science will also be considered, as appropriate. The successful applicant must possess excellent English verbal and written communication skills. Applicants are expected to have a very strong research background in the design and statistical analysis of functional brain-imaging experiments. Experience with SPM, FSL, Freesurfer, UNIX/LINUX/ and/or programming skills (MATLAB, C++; Python) are desirable and experience with MVPA or connectivity analyses a plus. Experience with pediatric functional neuroimaging and language and reading research are useful. Approximate start date is Spring/Summer 2013 (the earlier the better). Successful applicants will be appointed at Children's Hospital Boston and Harvard Medical School. For consideration please send a statement of interest, a CV and a list of three potential referees via email to Nadine Gaab, PhD (nadine.gaab(a)childrens.harvard.edu<mailto:nadine.gaab@childrens.harvard.edu>). The search will continue until the position is filled. -- "If we knew what it was we were doing, it would not be called research, would it?" A. Einstein (1879-1955) Nadine Gaab, PhD Assistant Professor of Pediatrics Harvard Medical School Faculty Affiliate Program in Neuroscience, Harvard Medical School Member of the Faculty of Education Harvard Graduate School of Education Children's Hospital Boston Department of Medicine/Division of Developmental Medicine Laboratories of Cognitive Neuroscience 1 Autumn Street (Office 643) Boston, MA 02115 nadine.gaab(a)childrens.harvard.edu<mailto:nadine.gaab@childrens.harvard.edu> phone: (857)-218-3021 Main Lab: 617-355-0400 fax: 617-730-0518 http://www.childrenshospital.org/research/gaablab www.babymri.org<http://www.babymri.org/>

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Export wmparc to table
by Mohammed Goryawala 27 Feb '13

27 Feb '13

Hello FreeSurfer experts, I want to export the white matter volumes from the wmparc stats file to a table. I cannot find the information on the wiki page. Thanks for your help. Dr. Mohammed Goryawala Center for Advanced Technology and Education Miami, Florida

2 1

default lateral extent corpus callosum
by Gonzalo Rojas Costa 27 Feb '13

27 Feb '13

Hi: What is the default thickness of the corpus callosum?... 5 mm ?... 2 mm for each side from midline ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Re: [Freesurfer] aseg.mgz display only left hemisphere
by Azeez Adebimpe 27 Feb '13

27 Feb '13

Hi Bruce, Thank for your response. I am trying to separate white matter, gray matter and csf from aseg.mgz base on the intensity values of subcortical tissues. My aim is to have GM, WM and CSF of both hemispheres not only left hemisphere, is it possible? Azeez .....Hi Azeez no, both hemispheres should be labeled by default. Are you sure it's not just the colors that are confusing you? The left hemi WM is shown in white by default, but if you mouse over it in freeview or tkmedit it should show the label Left-Cerebral-White-Matter.cheers Bruce On Tue, 26 Feb 2013, Azeez Adebimpe wrote:Hi freesurfer experts, The output of the segmentation, aseg.mgz only display right hemisphere. I used option -all in the segmentation. How can I make the both hemispheres visible or is there any specific option to choose for segmentation to make both hemispheres visible? Thank you/ Azeez Adebimpe _______________________________________________ Freesurfer mailing list Freesurfer(a)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. Azeez Adebimpe

2 1

(no subject)
by LE RESTE Pierre-jean 27 Feb '13

27 Feb '13

Hi, I would like to "sculpt" a label according to Talairach coordinates, precisely to cut the anterior part of the rostral middle frontal gyrus after +50mm AP; how would you procede ? Thank you for your software and thank you in advance for your help ! Yours sincerely, Pj Le Reste

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Freesurfer February 2013