[Freesurfer] acceptable T1 input sequences

Dear all, I am a new FreeSurfer user, and have a quick question before beginning to process T1 data: on the beginners guide (entitled 'Cortical Reconstruction with FreeSurfer'), it says that the input ought to be from MPRAGE or from SPGR sequences. 1) Are these the only sequences that FreeSurfer

Re: [Freesurfer] acceptable T1 input sequences

Hi Narly, 1) we've run a couple of mdeft and they seem fine. 2) It really depends on the CNR. The tools are much more robust these days, and a single acquisition is usually fine. It also depends on what you want to do with the data. If it's just for analysis of functional data then the requir

Re: [Freesurfer] acceptable T1 input sequences

Hi Bruce, Thanks for your answers. It actually is for a thickness study. I hope that one run will be adequate. Are there validity checks for the analysis output? thanks again, Narly. On Mon, 9 Jul 2007, Bruce Fischl wrote: > Hi Narly, > > 1) we've run a couple of mdeft and they seem fine. >

Re: [Freesurfer] acceptable T1 input sequences

the easiest thing is just visual inspection. It depends on the coil and the field strength. We routinely do a single 6.5 minute acquisition with a 12 channel coil at 3T and it seems fine. You could do test/retest studies of course, but that will tell you reliability, not sensitivity. Bruce On

[Freesurfer] Retinotopic mapping: fMRI analysis help?

Hi, I am hoping to perform a retinotopic mapping fMRI study. My paradigms consist of a reversing checkerboard annulus which increases and decreases in size and a reversing checkerboard wedge which moves clockwise dor 180 degrees and then anticlockwise. I am struggling to correctly perform the

[Freesurfer] mean thickness of whole cortex

Hello, Group Could anybody please tell me how to get the mean thickness of whole cortex? I got only the average thickness of each hemisphere with mris_anatomical_stats -a subject/lable/lh.aparc.annot -b subject lh Thank you in advance, Xin Wang ___

Re: [Freesurfer] mean thickness of whole cortex

you mean of both hemispheres together? We don't explicitly compute it, but the mean of the two hemisphere means should be pretty close, since they are similar in size On Mon, 9 Jul 2007, Wang, Xin wrote: Hello, Group Could anybody please tell me how to get the mean thickness of whole cortex

Re: [Freesurfer] Retinotopic mapping: fMRI analysis help?

Hi John, you would use a sine and cos at the fundamental. Unfortunately, our retinotopy analysis is rather finnicky about the data formats and directory structure, so you might want to use the FreeSurfer functional analysis tools. It's on my list to generalize it ... doug McLean John (NHS G

[Freesurfer] FreeSurfer relevance for studying structures other than the brain

Greetings, I am attempting to use FreeSurfer/Slicer to study data from a mass sprectrometer. To be of use, the segmentation capability of FreeSurfer/Slicer has to be based on quantitative data, not morphology. It appears as if FreeSurfer uses a generic mapping of the brain's structure as a st

[Freesurfer] Is converting to mgz conducive for 16-bit files?

Greetings, The data at this lab initially comes in a RAW data format. When converted to 16-bit TIFF files, the quantitative data is retained. I recognize that, in order for FreeSurfer to be of use, this data must be converted to mgz files. However, does the process of converting this informa

[Freesurfer] between group contrast using glmfit

Hello, I ran a group contrast in an ROI, correcting for multiple comparisons using the cluster size threshold method. It seems to have worked, however the one element that I don't understand as well is the basic between group contrast using an fsgd file, so I'm wondering if my commands real

Re: [Freesurfer] between group contrast using glmfit

The contrast is not specified in the fsgd. The fsgd just declares that you have two classes. The contrast is specified in your .mat file. The +1 -1 means that you will subtract ASD from Normals. doug Robert Levy wrote: Hello, I ran a group contrast in an ROI, correcting for multiple compari

[Freesurfer] export mgz+label to dicom files

Hi All: After imposing labels to a T1.mgz files in tkmedit, is it possible to write out dicom files with the label? Thanks in advance! Tao ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fr

Re: [Freesurfer] FreeSurfer relevance for studying structures other than the brain

Hi Greg, what structures exactly are you interested in? For the most part, we only do brain and brain-related structures (eg, ventricles). I don't know about Slicer, but FreeSurfer only handles T1-weighted MRI data. doug Greg Soltis wrote: Greetings, I am attempting to use FreeSurfer/

Re: [Freesurfer] Is converting to mgz conducive for 16-bit files?

The conversion to mgz is lossless. Having said that, at some point along the freesurfer stream, it does get converted to 8bit, but you can always get back to the original data. doug Greg Soltis wrote: Greetings, The data at this lab initially comes in a RAW data format. When converted to 1

Re: [Freesurfer] export mgz+label to dicom files

Sorry, we do not have an option to write out dicoms. doug T. Song wrote: Hi All: After imposing labels to a T1.mgz files in tkmedit, is it possible to write out dicom files with the label? Thanks in advance! Tao ___ Freesurfer mailing list Freesu

[Freesurfer] add the gray matter

Hello, Group I need to edit the pial surface. I learned to remove points with tkmedit from the tutorial. But how to add gray matter in the pial surface? Thank you in advance. Xin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://m

[Freesurfer] Re: Freesurfer Digest, Vol 41, Issue 13

hat point). At least for my data, acquired with surface coils, sub-optimal intensity correction is really annoying. ahoi & good luck Sebastian Thank you in advance. Xin -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.e

Re: [Freesurfer] add the gray matter

it depends why it's not getting out far enough. Usually you need to add control points in the nearby white matter that are <110 on the brainmask.mgz volume. On Mon, 9 Jul 2007, Wang, Xin wrote: Hello, Group I need to edit the pial surface. I learned to remove points with tkmedit from the

Re: [Freesurfer] Re: Freesurfer Digest, Vol 41, Issue 13

point). At least for my data, acquired with surface coils, sub-optimal intensity correction is really annoying. ahoi & good luck Sebastian Thank you in advance. Xin -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.