[Freesurfer] DicomSorter

Hallo, does somebody know, if there exist a similar program as DicomSorter for Linux, that organize that images and put it in the right folders? I run both, Windows and Linux on diferent parititions and its always a time spending thing to load into windows just for DicomSorter...I tried to inst

[Freesurfer] sequence]

Hello all, I’m a new user of FreeSurfer. We would like to start processing a large number of the scans. We have acquired three different sequences using a 1.5T GE scanner (a three dimensional T1-weighted SPGR sequence, and two dimensional PD and T2 sequences). We have already processed those s

Re: [Freesurfer] sequence]

Hi Roberto, most of our stuff only works on the T1 (i.e. option 1). In general the T2/PD is impossible to register accurately to the T1, which is why we haven't used it in the past. We have some new sequences developed by Andre van der Kouwe that resolve this problem, but they aren't widely us

Re: [Freesurfer] DicomSorter

Try using unpacksdcmdir and specify dicom as the output format. It will also do conversions to various formats too. doug Thomas Doering wrote: Hallo, does somebody know, if there exist a similar program as DicomSorter for Linux, that organize that images and put it in the right folders? I ru

[Freesurfer] make_average_subject

Dear List, Awhile back Cameron Ellis wrote to the listserv to ask about stats files for make_average_subject results. He was looking for information on the # of vertices and I believe he found another way to obtain that info. I would like to revert to his orginal question of whether there is a

Re: [Freesurfer] Retinotopy and MT+ localization analysis help

Hi Anisha, when you are debugging these things, it's best to go back as close to the raw data as possible (rather than looking at the final product on the flat map). Eg, try looking at the eccen and polar significance maps separately in the volume, then on the surface, then look at the phase ma

Re: [Freesurfer] make_average_subject

If you want to do stats on your cohort, you should use mris_preproc and mri_glmft using the same subject list as you used to create the average subject (you can pass all three programs an fsgd file to make sure that you have the same in both). mri_glmfit will give you mean and std thickness as

Re: [Freesurfer] Cluster thresholding

Hi all, I was hoping someone could help me with the problem below. I'm a little stuck on my analysis. Thanks, Alex > On 11/28/2007 07:43 PM, Alex Fornito wrote: >> Hi, >> I have run qdec for a simple contrast comparing thickness across the >> cortical surface between a patient and control group.

[Freesurfer] Error encountered while running selxavg3

Dear FreeSurfers, On my maiden voyage with selxavg3, I've encoutered an error and could use some help. After processing several subjects successfully, selxavg3 quit unexpectedly. Here is the exact message: Warning: matrix is singular to working precision > In fast_selxavg3 at 208 ntptot

Re: [Freesurfer] Cluster thresholding

Thanks for your help Pratap. I've actually been trying to follow the tutorial and was running simulations initially, but when I tried to re-trace my steps I ended omitted them because I forgot they were necessary for mri_surfcluster. Either way, the results are the same- I still get one who