Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

Training-Control Group Comparison Analysis
by Ryan 24 Oct '12

24 Oct '12

Hello everyone, I'm conducting an analysis involving a training group and a control group, where each group has a pre and a post scan. I setup the matrix file, the contrast file, and ran mri_glmfit along with mri_glmfit-sim for the cluster correction. The analysis finished revealing a significant cluster, although I want to confirm that my interpretation of the results is correct. I see a significant cluster which I believe means the training group showed greater thickening compared to the controls, is this correct? Also, how can I tell if clusters represent thickening or thinning in the training group compared to the control group? When I setup the matrix file, I entered 1's and -1's for the control subjects in the first column, and training subjects in the second column. When I setup the contrast file, I entered a -1 and then a 1, with 0's for the rest of the variables. Thanks for the help. -W. Ryan McGarry

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direct repositioning
by pietro de rossi 24 Oct '12

24 Oct '12

Hi FreeSurfer people, I'm considering editing through direct repositioning in freeview (under tools->reposition surface) for some scans. After that, do I need to rerun everything through the whole recon-all pipeline? What would be the command line for that? Thank you very much, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

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Re: [Freesurfer] Changes to Sub-cortical Structures after adding WM control points
by Mark Fletcher 23 Oct '12

23 Oct '12

Do you know when the next version is slated to launch? That being said, if I wanted to salvage my work so far, is it best to just use the original "subcortical" output as is (if I was not trying to change it in the first place?). -Mark Fletcher On Wed, Oct 17, 2012 at 12:01 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Mark > > it's hard to say if it's a "bug", but it is definitely a change in > behavior that will go away with 5.2 (that is, we will no longer > regenerate the aseg when you add control points). > > cheers > Bruce > On Wed, 17 Oct 2012, Mark > Fletcher wrote: > > > Dear FreeSurfers, > > > > After adding WMCP to a number of my subjects (which corrected the > problem), > > I retrieved to cortical and subcortical volumes from my subjects using > the > > "aparcstats2table". I had used "aparcstats2table" before and after adding > > the control points. Accurately, the regions I wanted to change, did > change > > in volume. However, the subcortical volumes post WMCP changed a lot as > > well? Some regions changed more than 20% after adding WMCP to other > > regions? Is this normal? Should I go with the original "subcortical" > > segmentation volumes, or the new ones? Is this part of the known bug in > > version 5.1.0 mentioned in the release notes about "running recon-all" a > > second time? Please advise? > > > > Sincerely , > > Mark Fletcher > > > > > > > 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. >

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Extract a color table from an annotation
by Anisha Keshavan 23 Oct '12

23 Oct '12

How do I extract a color table from an annotation? Thanks, Anisha

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Running gcut fails to create brainmask.gcuts.mgz
by Vincent 23 Oct '12

23 Oct '12

I'm attempting to remove some dura which is affecting my surfaces, but upon completion of running gcut I can see no differences in my images, nor can I use tkmedit to view my T1 with brainmask.gcuts.mgz, because it says it "couldn't import the segmentation volume". I looked for brainmask.gcuts.mgz but using ls recursively and grepping for it, but I can't find it anywhere. What explanations might there be for this? Thank you in advance. ::vincent

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Dealing with MS lesions
by Julio Alberto González Torre 23 Oct '12

23 Oct '12

Hi. My question is about dealing with multiple sclerosis lesions in white matter. I have previously worked with this sample in SPM8, and I have a binary mask for each subject with the white matter lesions marked. Instead of painting manually each lesion with the freesurfer interface, could I provide to the freesurfer the T1 images with the lesions painted with another program? (exactly, with the IMcalc of SPM, to set lesion values of each T1 image to a standard WM value according to the binary mask). Is this procedure correct? What value should I provide to this lesions? Thanks.

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MEMPRAGE
by Gina Caetano 23 Oct '12

23 Oct '12

Dear FreeSurfers, I am processing MEMPRAGE images: 1) I use the RMS (of the echoes) output from the scanner 2) the echoes were converted to mgz format [memprage_echo1(to4).mgz], conformed to 256³ , 1mm isotropic, and no further processing. 3) I ran the mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh, and got new files as output (?h.white_addedname, ?h.pial_addedname etc) However, I expected to have more of the dura discarded from the ?h.pial boundaries as what I am getting May I be missing something in the processing of this type of images? How can I improve the output? Thank you in advance, Gina

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trac-all -prep error during inter-subject registration with mri_cvs_register
by Verena Gramse 23 Oct '12

23 Oct '12

________________________________ From: Verena Gramse Sent: Monday, October 22, 2012 8:19 PM To: freesurfer(a)nmr.mgh.harvard Subject: trac-all -prep error during inter-subject registration with mri_cvs_register Dear Tracula Team, I have been running into problems during Inter-subject registration at the mri_cvs_register step: it aborts with Image Exception : #22 :: ERROR: Could not open image /gablab/p/BGFU/data/freesurfer/cvs_avg35/mri//norm.mgz. But norm.mgz exists at the specified location and it can be opened with freeview without problems. Did I oversee anything? Thanks in advance! Verena Find attached my dmrirc and the error.log

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relationship between cortical volume, cortical area and cortical thickness
by L. Koenders 23 Oct '12

23 Oct '12

Dear Freesurfer people, We posted this question before, but maybe you missed it. We have a question regarding the relationship between cortical volume, cortical area and cortical thickness measurements derived from the parcellation stat-file. We were under the impression that the volume is equal to the area*thickness. However, this is not the case. Can you tell us how these three measurements relate to each other? Thanks for your help! Kind regards, Marise Machielsen & Laura Koenders ________________________________ AMC Disclaimer : http://www.amc.nl/disclaimer ________________________________

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AAL labels
by MCLAREN, Donald 23 Oct '12

23 Oct '12

Has anyone created an AAL label file for Freesurfer? I've done some ROI analysis using AAL regions and want to display regional values on the freesurfer surface. 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.

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