Re: [Freesurfer] retinotopic mapping selxavg3-sess error

Sorry for the delay. I'm new to FSL, Freesurfer, and VB, so maybe I'm doing it wrong, but I have the impression I cannot run FSL from the VB: - Typing 'fsl' yields 'fsl: Command not found'. - Checking the environment with 'echo $FSLDIR' yields 'FSLDIR: undefined variable' - Checking the path with

[Freesurfer] Error for mri_glmfit contrast

Dear Freesurfer experts, I am currently trying to do a cortical thickness group analysis with one factor, three levels . I have run mri_preproc and mri_surf2surf, and am now trying to run mri_glmfit --y lh.group.thickness.10B.mgh --fsgd easy2.file --C contrast1.mtx --surf fsaverage lh

[Freesurfer] problem with surface area regression

Dear Freesurfer, I have checked the mail list, none could answer my problem. I added up the value of all vertxes in the .area or .area.pial files, find that brain size did not contribute much to that vertex-sum. However, some experiment used total brain volume as a regreesion

Re: [Freesurfer] lme issues + failure to converge

Hi Cathy If you only have three groups in your data (Control subjects, High risk patients, Ill patients) then you should drop the “Controls versus all others and controls*time interaction” terms from your design matrix. Otherwise it is ill-conditioned. One way to check your design matrix is

[Freesurfer] mri_glimfit paired analysis

Dear FreeSurfers I'm using Freesurfer 5.1 on Ubuntu 12.04 LTS. Currently running paired analysis as described here https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis After mri_glmfit \ --glmdir lh.paired-diff \ --y lh.paired-diff.thickness.sm05.mgh \ --fsgd paired-diff.fsgd \ --C

Re: [Freesurfer] Help with QDEC error

Hi Nick and Doug,  Can you suggest an alternative way if QDEC is unable to handle a single group?   I would like to run these analyses to address reviewers comments.   Best, Manish From: Douglas Greve gr...@nmr.mgh.harvard.edu To: Manish Dalwani

[Freesurfer] Is there any way of finding out RESEL number in the GLM output?

Hello Freesurfer users, I'd hope to know the RESEL number in my group GLM analysis data. I can calculate the number of vertices and also see the fwhm.dat in the ouput GLM folder, but I wonder if there is anyway of finding out RESEL size if freesurfer also provides that info like SPM does. -Glen

[Freesurfer] retinotopy betas

Hi, I am examining the affect a metal artifact has on fMRI data, and I am using Eccentricity mapping with the retinotopy analysis in FSFast. I was recently asked to switch from examining the difference in the fsig to examining the difference in the betas. I opened up beta.nii.gz and I can see

[Freesurfer] [FreeSurfer] Freeview: Invalid drawable

Dear Koen, Freeview returns 8 lines of the error message invalid drawable whenever executed. The messages are as follows 2013-06-24 14:24:57.930 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.931 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.944 Freeview[1937:303] invalid

[Freesurfer] infant .tiff templates

Hello freesurfers, I am currently attempting to create my own .tiff templates for a series of infant fMRI's (neonates, 1 yr olds, and 2 yr olds). I currently have the templates in .nii.gz, .mgz, and .img/.hdr formats. Is there any easy way to convert from one of these formats to a .tiff

[Freesurfer] Question about running kvlQuantifyHippocampalSubfieldSegmentations.sh

Hi all, I am getting error messages while running kvlQuantifyHippocampalSubfieldSegmentations.sh, similar to the error mentioned in an earlier email (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg24430.html). We did use the -hippo-subfields flag for all of our subjects first,

Re: [Freesurfer] infant .tiff templates

Hi Mark can you clarify what you mean? What template are you referring to? Bruec On Mon, 24 Jun 2013, Mark Plantz wrote: Hello freesurfers,       I am currently attempting to create my own .tiff templates for a series of infant fMRI's (neonates, 1 yr olds, and 2 yr olds). I currently have

Re: [Freesurfer] Multiple inputs into recon-all -i

Hi Ye you only need to give it a single file from each run and it will find the rest. The only time you use -i more than once is if you acquired more than 1 T1-weighted volume. Definitely don't give it all the files that make up the same volume cheers Bruce On Mon, 24 Jun 2013, ye tian

Re: [Freesurfer] Multiple inputs into recon-all -i

Dear Bruce, Thank you very much for your suggestion, but I am afraid that I still don't quite understand you. In order to make it simple, suppose I have two files, Barba001.IMA and Barba002.IMA, coming directly from the scanner. Now if I enter *recon-all -s Barba -i Barba001.IMA* from the

Re: [Freesurfer] Multiple inputs into recon-all -i

Hi Ye, you would never have two files, as each file represents one image, or slice from a sequence. So you might have two sequences of files, say Barba001-1.img, Barba001-2.img... Barba001-256.ima, and Baraba002-1.ima, Barba002-2.ima Barba002-256.ima. Then you would use -i twice, once

Re: [Freesurfer] Multiple inputs into recon-all -i

Dear Bruce, Thank you very much! Sincerely, Ye On Mon, Jun 24, 2013 at 7:32 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Ye, you would never have two files, as each file represents one image, or slice from a sequence. So you might have two sequences of files, say Barba001-1.img,

Re: [Freesurfer] Fwd: DTI questions

Sorry, can't open the image. On Sun, 23 Jun 2013, Rotem Saar wrote: Hi there, Long time:). Well I wrote to the list several times regarding high FA values I got when performing DTI analysis. Today we know that the problem was an additional direction (we had 17 directions instead of 16 - we

Re: [Freesurfer] Fwd: DTI questions

Hi Rotem - No problem. Were these scans by any chance acquired with a coronal slice prescription? In the axial views that you sent, the artifact that you're pointing to looks like misalignment between consecutive coronal slices, which could be due to head motion. a.y On Tue, 25 Jun 2013,