Freesurfer April 2014

freesurfer@nmr.mgh.harvard.edu

147 participants
229 discussions

Re: [Freesurfer] mri_glmfit | constructing the "C.txt" and FSGD files
by Baker, Justin T.,M.D.,Ph.D. 24 Apr '14

24 Apr '14

Hi Freesurfer et al., Since no one has responded to my email below, I'll assume my question is poorly formed. I'm trying to compose an appropriate contrast matrix (what I've called the "C.txt" file) for a regression of surface thickness categorical comparison (two categories) with two nuisance variables. Can someone clarify what each column of the contrast file represents and how to set it up for this? I'm having trouble finding documentation of this. It is my hope that when I call: mri_glmfit --fsgd fsgd.txt --y lh.TEMP.mgh --C C.txt --surf fsaverage lh --cortex --glmdir lh.TEMP.output I am prepping to run a regression looking at the relationship between Patient status (i.e. 1 or 0) and cortical thickness, partialing out age and gender. Thanks in advance for any help you can offer, Justin On Apr 23, 2014, at 3:40 PM, Justin Baker <jtbaker(a)partners.org> wrote: > Hi all, > > I'm trying to run what should be a very simple cortical thickness regression analysis in mri_glmfit, but could use some help with putting together my "C.txt" and FSGD files. > I have two classes (e.g. Patient, Control) and two nuisance variables (i.e. Age, Gender). > > My FSGD file looks like this: > GroupDescriptorFile 1 > Title FS_Thickness > Class Patient > Class Control > Variables Age Gender > Input 130725_GB49NP Patient 18 1 > Input 130620_HU64KP Patient 21 2 > ... > > And my "C.txt" file looks like: > 1 -1 0 0 0 0 > ...which I'm pretty sure is wrong, but I don't quite understand what the columns mean, so any light shed would be appreciated! > > -Justin

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FS QA Tools: Output, html and .gif Files
by Jessica Bernard 24 Apr '14

24 Apr '14

Hi All, I've been running the Freesurfer QA Tools on some new data, and have been having some difficulties with the outputs. I am running this using the -snaps-detailed flag. In the past, we have had .html links, but also detailed .gif files for each person. We've consistently had trouble with the .html links, but the .gif files have been perfectly fine. However, when running new individuals, not only are the images broken in the .html output, but there are no gif files (which are preferred). Is there an additional command that needs to be added to generate the detailed gif files as well? Sorry if this is a rather basic question. I recently took over the Freesurfer QA process, and am relatively new to the functions, and my predecessor does not know how they created the gif files (the first batch of QA was run 6 months ago with our first wave of data collection). Thanks in advance for any help you may be able to provide. Best Wishes, Jessica

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mri_segstats question
by pfotiad＠nmr.mgh.harvard.edu 24 Apr '14

24 Apr '14

Hi FS community, I had some questions regarding the mri_segstats command: 1) In the excludeid flag, are the ids the ones shown in the FreeSurferColorLUT.txt? 2) In case I would like to measure the mean intensity of the orig file as outlined in the second example in https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats: mri_segstats --seg $SUBJECTS_DIR/bert/mri/aseg --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --nonempty --excludeid 0 --sum bert.aseg.sum --in $SUBJECTS_DIR/bert/mri/orig is the --seg flag necessary in order to calculate only the mean intensity within the skull, or does it serve another purpose? Thanks in advance, Panos

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V1 label
by krista kelly 24 Apr '14

24 Apr '14

Hello, I am looking at cortical thickness and surface area using Freesurfer. I have transferred label V1 from freesurfer onto the brains of my participants and when I view them on the inflated brains in tksurfer , I notice that there are holes in the label. Is this an issue when calculating mean cortical thickness and total surface area estimations? Should I fill these in somehow? I've attached a picture to show as an example. Please let me know if the picture cannot be viewed. Thanks! Krista

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gPPI Toolbox Version 13.1 for SPM has now been released
by MCLAREN, Donald 24 Apr '14

24 Apr '14

Version 13.1 of the gPPI toolbox (previously released versions were 7.12 and 13) is now available at http://www.nitrc.org/projects/gppi Version 13.1 now supports task-models from FSFAST and can read the model structure directly from your FSFAST analysis. Version 13.1 now support robust weighted least squares (rWLS) - requires your first level model to have been generated with the rWLS toolbox. The major changes are: (1) Integrated spm_spm and spm_spm_WB into the software, no patch is needed. P.wb=1 will use the whole brain approach. (2) Added ability to start with FSFAST first level models. (3) Added ability to do rWLS, if the rWLS was used in the first-level models. (4) Removed dependency of gzip on java. (5) A few other bells and whistles. (6) Added script to pre-extract VOI timeseries (7) Added the ability to use upsampled data or neural signal inputs 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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Freesurfer, merci de m'ajouter à votre réseau LinkedIn
by LAOUCHEDI MAKHLOUF via LinkedIn 24 Apr '14

24 Apr '14

LinkedIn ------------ LAOUCHEDI MAKHLOUF souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Freesurfer, J'aimerais vous inviter à rejoindre mon réseau professionnel en ligne, sur le site LinkedIn. LAOUCHEDI Accepter l'invitation de LAOUCHEDI MAKHLOUF http://www.linkedin.com/e/-qq80um-hue3y8a5-y/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59… Voir le profil de LAOUCHEDI MAKHLOUF http://www.linkedin.com/e/-qq80um-hue3y8a5-y/rso/85174646/IQTY/name/6647116… ------------------------------------------ Vous recevez des invitations par e-mail. Cet e-mail est destiné à Freesurfer List. Découvrez pourquoi nous avons inclus ceci : http://www.linkedin.com/e/-qq80um-hue3y8a5-y/plh/http%3A%2F%2Fhelp%2Elinked… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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Applying a precomputed transform matrix to an image in free surfer
by Emad Ahmadi 23 Apr '14

23 Apr '14

Hello, I’m having a volume (e.g. dtifit_FA.nii.gz) and a transform matrix (e.g. diff2anatorig.bbr.mat), and I want to apply the transform matrix to the image and generate a transformed image. This is a general question I’m having, but in this particular case, I want to apply the transform matrix (from diffusion space to the anatomical space generated by TRACULA) to the FA map to generate a transformed FA map that can be overlaid on the anatomical images. I wonder if I have to use mri_vol2vol command for doing this, and I don’t know how to provide it with appropriate flags. I’m already having the transform matrix generated by TRACULA (and I don’t want to change it; I just want to apply it to the image!). My crude guess would be something like this: mri_vol2vol --mov <address of dtifit_FA.nii.gz> --o <address of transformed_dtifit_FA.nii.gz> --reg diff2anatorig.bbr.mat Please let me know how I should run this command. Thank you very much, Emad P.S. I know that for this particular example, I can use the anatomical images in dlabel/diff, but the point for me is to learn how to apply a transform matrix to an image and generate a transformed image in freesurfer Emad Ahmadi, MD ----------------------------------------------- Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad(a)nmr.mgh.harvard.edu

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Tumor Segmentation in FreeSurfer
by Mohammed Goryawala 23 Apr '14

23 Apr '14

Hello, I am reposting this question since I have not received any feedback with this issue. I am interested in understanding if tumor segmentation can be carried out using FreeSurfer. On examining the stats file we do see a tumor volume reported. I was wondering how this is calculated. Thanks Mohammed

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Subfields on 1.5 Tesla
by Alan Francis 23 Apr '14

23 Apr '14

Hi Koen & FreeSurfers: I have received a manuscript to review for possible publication. The authors have used the subfields algorithm on 1.5T scans and obtained a parcellation with values. They have drawn some major conclusions on the basis of the findings. My understanding is that this method can only be done on 3T. Is the 1.5T results valid? Please advice. thanks, Alan Francis

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Re: [Freesurfer] mri_convert Siemens .IMA error
by Douglas N Greve 22 Apr '14

22 Apr '14

Hi Paul, I was finally able to track down the bug. You can get a new version from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mri_conver… copy it to $FREESURFER_HOME/bin/mri_convert doug On 12/08/2013 06:28 PM, prasser wrote: > Hi Doug, > > Sorry for the delay. Please find 1.IMA attached. > > Thanks, > Paul > > > ---- On Fri, 06 Dec 2013 13:15:29 -0800 *Douglas N Greve > <greve(a)nmr.mgh.harvard.edu>* wrote ---- > > > Can you upload a single dicom file to me? One should be enough > > On 12/06/2013 04:02 PM, Paul Rasser wrote: > >> > >> We are using Freesurfer5.3 on os x 10.8. > >> > > > > > > On 6 Dec 2013, at 2:19 pm, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > >> > >> This may be a known problem. What version of FS are you using and > >> what is your platform? > >> doug > >> > >> > >> > >> > >> On 12/5/13 3:26 PM, prasser wrote: > >>> Thanks, but the orientation shift appears as a skew. Also, we > don't > >>> have any fiducial markers for this group of scans so it would > be a > >>> little tricky to confirm the correct application of > >>> -out_orientation. I would rather let mri_convert handle this from > >>> the .IMAs. > >>> > >>> Is there any additional information I can provide from from > the .IMA > >>> header etc that could shed some light on why mri_convert is > behaving > >>> in this way? > >>> > >>> Thanks, > >>> Paul > >>> > >>> > >>> > >>> ---- On Wed, 04 Dec 2013 22:11:27 -0800 *Mark Plantz > >>> <markplantz2016(a)u.northwestern.edu > <mailto:markplantz2016@u.northwestern.edu>>* wrote ---- > >>> > >>> Not sure if this helps, but you can alter the output orientation > >>> using the flag "--out_orientation" followed by LIA (for > >>> example). Maybe the input file needs to be in a specific > >>> orientation before it can be converted properly. > >>> > >>> > >>> On Wed, Dec 4, 2013 at 9:56 PM, prasser <prasser(a)zoho.com > <mailto:prasser@zoho.com> > >>> <mailto:prasser@zoho.com>> wrote: > >>> > >>> Hi, > >>> > >>> I'm currently having problems converting .IMA files > >>> collected from a Siemens Skyra to .mgz format using > >>> mri_convert from Freesurfer5.3 on os x. > >>> > >>> Using: > >>> > >>> mri_convert -it siemens -ot mgz 1.IMA test.mgz > >>> > >>> I get the error message: > >>> > >>> does not contain a Siemens ASCII header has this file been > >>> anonymised? > >>> > >>> ERROR: cannot unpack mosiacs without ASCII header > >>> > >>> The .IMA files have been taken straight from the scanner > >>> console. > >>> > >>> If I try: > >>> > >>> mri_convert -it dicom -ot mgz 1.IMA test.mgz > >>> > >>> this creates the .mgz, however there is an orientation shift > >>> and a vertical stripe artefact appears in the sagittal view > >>> (please see attached) when compared to the original .IMA. > >>> > >>> Any suggestions on how to convert the Siemens .IMA files > >>> correctly? > >>> > >>> Thanks, > >>> > >>> Paul > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)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 > >>> > >>> > >>> 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(a)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 > >>> > >>> > >>> 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(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)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 > >> > >> > >> 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. > > -- > 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 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Freesurfer April 2014