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Comparing thickness at vertex level
by Gabriel Gonzalez Escamilla 24 Oct '12

24 Oct '12

2 1

Total cerebral volume.
by Zheng Hui 24 Oct '12

24 Oct '12

Hi freesurfer, We are trying to calculate the total cerebral volume which excludes cerebellum, brainstem, ventricle and CSF from the aseg.txt. Do we use CortexVol + CorticalWhiteMatterVol + SubCortGrayVol Or CortexVol + CorticalWhiteMatterVol + Sum(all structures (after ICV in the list) except ventricle, CSF, cerebellum and brainstem) Also, I saw Doug's post about the bug fixing for SupraTentorialVol. To re-run the segstats for longitudinal subjects, any extra step other than "recon-all –long tpN baseID –segstats" and does it affect any other structure or just SupraTentorialVol? Thank you, Zheng Hui

2 1

Re: [Freesurfer] AAL labels
by Garikoitz Lerma-Usabiaga 24 Oct '12

24 Oct '12

Hi! Well, as far as I know: - both are MNI standards ---- Colin27 is the MNI Colin27 single subject standard ---- fsaverage is MNI305 My problem with fsaverage was that I couldn't use the transformations made with the registration matrix after spmregister or bbregister, but I understand that it depends on the application. This is the reason I used the alternative way through Colin27 (since both are the same brain, one in 2mm and the other in 1mm, the registration matrix was almost 1). Saying that, I understand that if you want the AAL .labels in fsaverage, you always could use mri_label2label in order to transform every label to fsaverage. I don't know what is the best method, maybe some expert in the list will be able to confirm this step, but it is definitely what I would do. If you are thinking using qdec or some other tool with fsaverage, I understand that you could always create your own average and transform the data there or create the data with mri_surf2surf for Colin27 (this is going to be our approach). hope this helps! Gari On Tue, Oct 23, 2012 at 7:15 PM, MCLAREN, Donald <mclaren.donald(a)gmail.com>wrote: > How does the Colin 27 space differ from MNI space in terms of > freesurfer? Ideally, I'd want them to be useable with the standard FS > Average surface that is in MNI space. > > 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 Tue, Oct 23, 2012 at 7:37 AM, Garikoitz Lerma-Usabiaga > <garikoitz(a)gmail.com> wrote: > > Hi Donald and everybody, > > I created AAL .mgh and .label-s in FS Colin27 space, if anybody is > > interested please drop me a line. > > > > best regards! > > Gari > > > > On Thu, Jul 12, 2012 at 11:12 PM, MCLAREN, Donald < > mclaren.donald(a)gmail.com> > > wrote: > >> > >> 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. > >> _______________________________________________ > >> 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. > >> > > >

2 1

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

2 1

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. >

3 2

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

2 1

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

2 1

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.

2 3

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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