Re: [Freesurfer] mri_convert

it could be that the info needed to create the orientation info is not in the dicom. You can also try it without the -it dicom. You can also specify an orientation like --in_orientation RAS. This will probably be wrong, but it will at least let you see the image. On 7/19/17 8:44 PM, John

Re: [Freesurfer] mri_convert

Dear Dr Bruce, Thank you very much for your response. I tried mri_Convert -i INPUT_FIRST_DICOM -it dicom -ot nii -o OUTPUT_4d.nii The problem is when I run mri_info on the "OUTPUT_4d.nii" I get the following voxel-to-ras determinant 0 ras to voxel transform: mat =NULL! MatrixFree: NULL mat

Re: [Freesurfer] mri_convert

Hi Jon have you tried mri_convert? cheers Bruce On Wed, 19 Jul 2017, John Anderson wrote: > Dear Freesurfer, > Are there any tools in Freesurfer that can help to convert PET DICOMs to > nifti files? > > Thank you for your help and for any suggestion > Jon > > >

[Freesurfer] mri_convert

Dear Freesurfer, Are there any tools in Freesurfer that can help to convert PET DICOMs to nifti files? Thank you for your help and for any suggestion Jon___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] mri_glmfit-sim --grf question

Yes, that is expected with your command line. The issue is that you are using a positive (pos) a priori hypothesis about the sign of the effect. By default, freesurfer generates unsigned statistics (this is what you see when you just view the stats map). When you specify pos, it adjusts the

[Freesurfer] mri_glmfit-sim --grf question

Dear Freesurfer experts, I'm trying to run multiple comparisons correction using mri_glmfit-sim. Since I'm working with volume data, I used -grf instead of -cache. The resulting map has bigger clusters with higher significance values than the original sig.mgh map from mri_glmfit. Is this normal?

[Freesurfer] converting vertex numbers in .label files to R, A, S coordinates

Dear Freesurfer experts, My question concerns the .label files and the correspondence between the vertex numbers (in the first column) and the R,A,S coordinates. I have the R,A,S coordinates of voxels that I want to display on the surface. For this purpose, I created a label file with the

[Freesurfer] Custom Annotation: 1st Annot Visible in TKSurfer but not Freeview

Hi Ruopeng, That works perfectly, thanks so much. Best, Ursula --- Ursula Tooley Ph.D. Student Neuroscience Graduate Group University of Pennsylvania utoo...@gmail.com 202.413.5627 > > From: Ruopeng Wang > > Subject: Re:

[Freesurfer] Recon-all start point for pial, aseg, CP edits

Hi developers, I am working with scans from a group of patients that sometimes require pial edits, aseg editing (e.g. ventricle being labelled as amygdala), and control points to fix intensity normalizations. I am unsure as to which stage I should start the recon-all re-processing at so

Re: [Freesurfer] Switch FreeSurfer Desikan-Killiany atlas to Civet

Dear Antonin, I haven’t used CIVET myself, however, if I remember correctly it employs several metrics to estimate cortical thickness, referred to “Link”, “Laplace”, and “Average Near”. The latter one is a re-implementation of the one used in FreeSurfer. They are described and compared here:

Re: [Freesurfer] dmri_motion -T threshold

Can you send me an example of an image that has slices with drop-out, and for which the number of bad slices from dmi_motion is 0? From: > on behalf of "Buckless, Colleen"

Re: [Freesurfer] dmri_motion -T threshold

We want to match on dropout as well which would require us to change the threshold. How should the threshold value be determined in order for us to match on dropout? From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia

Re: [Freesurfer] Masking option for tractstats2table

Hi Derek – The version in the distribution is the only version that exists. One option for what you’re trying to do is to use the *.byvoxel.* stats files and average the values, say, in the first 1/3 of points. a.y From:

Re: [Freesurfer] dmri_motion -T threshold

If neither of your groups has bad slices (which you should confirm by looking at the images), then they are matched in that respect. You can then check for differences in the rotational and translational motion to see if any further matching is needed. From:

Re: [Freesurfer] dmri_motion -T threshold

Hi Anastasia, We are trying to match our groups on motion and can't match them if our scans have the floor values. We are not sure how to determine what the threshold value should be in order to make the dropout score no longer floor out. Any suggestions on how to better match on motion?

Re: [Freesurfer] SPC in surface area

Hi Alejandra, the script creates an SPC stack, where you have all the SPC values for each vertex for each subject. Even in without the stack the SPC values are stored in each base directory. There are probably ways to define a label based on your ROI, then you can do an ROI analysis on the