Freesurfer

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Re: [Freesurfer] mri_vol2surf or mri_cor2label
by Auer, Tibor 09 Aug '12

09 Aug '12

Hi, you should use mri_cor2label. Bests, Auer, Tibor M.D. Ph.D. Biomedizinische NMR Forschungs GmbH am Max-Planck Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Germany Phone/Work: +49-(0)551-201-1725 Phone/Home: +49-(0)551-387-0076 Mobile: +49-(0)176-8012-7921 Mail: tauer(a)mpibpc.mpg.de -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Stephanie Rossi Sent: Thursday, August 09, 2012 7:04 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] mri_vol2surf or mri_cor2label Hi, I have seeds defined in fsl for individual subjects (nii.gz) and I would like to convert them to freesurfer labels for individual subjects. Which command would I have to use: mri_vol2surf or mri_cor2label? Thank you for your help! Best, Stephanie _______________________________________________ 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.

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asking about seed/target ROIs in TRACULA
by Juke Cha 09 Aug '12

09 Aug '12

Hi, I'm wondering if I can get any information about ROIs being used in the global tractography procedure in TRACULA. I'm particularly interested in the uncinate fasciculus. I've searched for such information in the website and the article, to no avail. Thanks for your help! Best, Juke

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Making Anatomical Mass for optical data
by Mark Fletcher 09 Aug '12

09 Aug '12

Dear FreeSurfer Developers, Currently we are trying to analyze our functional data (optical imaging) using ROI’s that are defined on the basis of FreeSurfer Segmentation. In order to do this, we need a 3 dimensional mask in which a particular region as identified by FreeSurfer is used as a mask for analyzing our functional data. How can we output from FreeSurfer what each voxel is classified as (hippocampus, etc.), or a mask having a value of 1 for each region, and a 0 for every other voxel. Also, what coordinate space would this be in? We would prefer either MNI or TAI (or a way to get into either space). Thanks you so much for your help. Sincerely, Mark Fletcher CNL Lab UIUC

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Subcortical segmentations
by Jordan Pierce 08 Aug '12

08 Aug '12

Hi, I have a question about subcortical segmentations: there are a lot of places across subjects where the thalamus label seems to include white matter (images attached), am I right to think that this needs to corrected and is there any reason the program might do this so often? Thanks, Jordan Pierce

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Re: [Freesurfer] Freesurfer Digest, Vol 102, Issue 1
by Gibbard, Clare 08 Aug '12

08 Aug '12

Hi Doug, Thank you, that worked perfectly. Best wishes, Clare ________________________________________ Date: Tue, 31 Jul 2012 14:30:50 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all -qcache curvature error & recon-all make -all To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <5018245A.1050903(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Subject 20 is definitely out of synch, but the "make all" feature is not catching it. Try re-running this subject with -autorecon3 doug On 07/25/2012 11:45 AM, Gibbard, Clare wrote: > Hi Bruce, > > Thanks, I've attached the end of the recon-all.log file for one of the subjects (the whole thing was too large). This is what I get when I run recon-all -version: > $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ > > When I try to run recon-all -s subject_no -make all I don't think anything comes up in the log. I get this in the terminal window: > clare@clare-OptiPlex-990:~/subjects$ recon-all -s subject_20 -make all > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 > Subject 'subject_20': make all > make: Nothing to be done for `all'. > clare@clare-OptiPlex-990:~/subjects$ > > Let me know if you need anything else. Thank you. > > Best wishes, > Clare > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: 25 July 2012 14:44 > To: Gibbard, Clare > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Recon-all -qcache curvature error& recon-all make -all > > Hi Clare > > can you send us the screen output and also what version you are running? > > thanks > Bruce > On > Wed, 25 Jul 2012, Gibbard, Clare wrote: > >> Hello, >> >> I have run several scans using recon-all -all -subjid subject_no -expert >> expert.opts where my expert.opts file changes the parameters for the >> mri_normalize step (this works well in my scans). I then had to edit a few >> of the scans by adding in more white matter and a few control points. I >> re-ran them to incorporate the edits using recon-all -s subject_no -make all >> -xopts-use. This worked well. >> >> I then ran recon-all -s subject_no -qcache ready for doing a group >> analysis. I got an error reading the curvature file in those subjects I had >> edited. I can see from the mailing list that others have had this error >> previously and ran recon-all -s subject_no -make all to fix it. I tried >> this, but I got a message saying that there was nothing to be done for all. >> >> Are you able to advise me on what I can try now? Do I need to go back a >> step? >> >> Thank you very much, >> Clare

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Re: [Freesurfer] contrast matrix
by Douglas N Greve 07 Aug '12

07 Aug '12

Hi Meng, in the case of a 2x2 interaction, the F test has only 1 dof in the numerator. This makes it the same as an unsigned t-test. The interaction in intercept is just the interaction regressing out gender and age (the first row of your matrix). The interaction in slope is the 2x2xage interaction regressing out the effect of gender (the 2nd row). doug On 08/06/2012 10:28 PM, Meng Li wrote: > Hi professor, > I know that if performing the Analysis of Variance (eg. 2*2 > interaction analysis), we should use the F-test, so I wonder the > reason why the contrast matrix of 4G0V > (http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G0V) use the t-test. > And if I want to know whether there is an interaction between > diagnosis and genotype regressing out the effect of gender and age (in > either intercept or slope ??) as previous emial mentioned, that is > using the F-test to detect the interaction, so whether I should use > the following matrix: > 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 > Thanks, > Best wishes, > Meng > Date: Mon, 06 Aug 2012 10:01:22 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] contrast matrix > To: freesurfer(a)nmr.mgh.harvard.edu > Hi Meng, the first row is what you want. The second row tests for an > interaction between diagnosis, genotype, and age. > doug > On 08/04/2012 10:23 PM, Meng Li wrote: > > Hi Freesurfers, > > > > My experimental design includes 3 discrete factors and 1 continuous > > variables: > > > > Discrete factors: diagnosis with two levels (A, B); genotype with two > > levels (G, T); gender (F, M) > > > > Continuous variable: age > > > > So I can get 8 classes: AGF, AGM, ATF,ATM, BGF, BGM, BTF, BTM. Then I > > want to perform 2 (diagnosis)* 2(genotype) interaction analysis with > > regressing out the effect of gender and age. Is the following contrast > > matrix correct? > > > > 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 0 > > > > 0 0 0 0 0 0 0 00.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 > > > > Any help will be very appreciated. > > > > Best wishes, > > > > Meng > > > > > > > -- 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

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T1 space to DTI space
by Trietsch, Rayna 07 Aug '12

07 Aug '12

Hi, I am trying to go from T1 space to DTI space using fsl_rigid_register to co-register the T1 image to the b0 image. fsl_rigd_register gives me a matrix outputted as a .fslmat file. If I multiple that matrix by a matrix of the coordinates of my head points from tkmedit than I should get the coordinates which I can input into TrackVis but I get coordinates which are out of the xyz range of the image in TrackVis. Any ideas on what could be going wrong or another approach? Thanks! ~Rayna~

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lh.ROI45.label and lh.ROI44.label overlapping
by Garikoitz Lerma Usabiaga 07 Aug '12

07 Aug '12

Hi freesurfers experts, this is (please check attached image) the best I got when trying to map a volume ROI (BA45 in MarsBar = MNI_Frontal_Inf_Tri_L_roi) to freesurfer using mri_vol2surf. I used /freesurfer/average/mni152.register.dat instead of spmregister since the ROI was already in mni152 2mm, the registration was perfect -checked with tkregister2. - I obtained the red area of the image, which is outside of the ROI45.label. Considering that the source was not exactly the same, could I consider it acceptable for cortical thickness analysis? - Why are the 44 and 45 overlapping? Thank you very much and sorry for the multiple questions, Gari

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question about MNI coordinates or talariach coordinate in Qdec
by ZhiLiangLong 07 Aug '12

07 Aug '12

Hi all: In qdec, when i left-clicked on a point of pial surface, there would be a coordinate displayed at the bottom of qdec. my qestion is that does the coordinate belong to the MNI space or talariach space?

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aseg.stats ICV question
by Natalie Han 06 Aug '12

06 Aug '12

Hi, all, anyone knows that if the ICV in the aseg.stats means the whole volumes inside the skull or the total volumes of GM and WM? Does it include the CSF between the skull and the cortex? Thanks. Natalie

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