[Freesurfer] PhD position in tractography validation, Inserm U930 "Brain and imaging" lab, University François-Rabelais of Tours

"A funded PhD Student position will be available in the “Brain and Imaging” Inserm unit (national institute for health) settled in Tours, France, from October 1st, 2014 to September 30th, 2017. During this time period, the candidate will have: (1) to develop tools and pertinent criteria for com

Re: [Freesurfer] Resting State Networks on Cortical Surface

Hi Doug, A follow-up. I've gone back and re-done the registration using nifti file with the ICA20 maps. I noticed in tkregister2 that when I press on the TARGET tab there is extremely good alignment ( i think it is to 'orig.mgz' in the mri folder of my subject which I had processed using recon

[Freesurfer] Difference in Volumetric measure of Hippocampus Segmentation

Hello Freesurfer Expert, I am working on volumetric analysis of Hippocampus. When i am find the no of voxel's for left Hippocampus (17) and Right Hippocampus(53) using command i m getting some what diffrence. I just want to know which command should be used for the volumetric analysis: Lh

Re: [Freesurfer] Freesurfer 5.3 and CentOS 5.10

Zeke - Thank you for getting back in touch with me. I have since grabbed the source distribution to see if I can compile this beast on my own ... quite the arduous task indeed. It would be great to see the configure options that were used to create the public stable 5 release, still looking around

Re: [Freesurfer] Resting State Networks on Cortical Surface

On 3/6/14 6:39 AM, Xuelong Zhao wrote: Hi Doug, A follow-up. I've gone back and re-done the registration using nifti file with the ICA20 maps. I noticed in tkregister2 that when I press on the TARGET tab there is extremely good alignment ( i think it is to 'orig.mgz' in the mri folder of my

Re: [Freesurfer] Difference in Volumetric measure of Hippocampus Segmentation

The one from asegsats2table takes into account partial volume information doug On 3/6/14 7:13 AM, Saurabh Thakur wrote: Hello Freesurfer Expert, I am working on volumetric analysis of Hippocampus. When i am find the no of voxel's for left Hippocampus (17) and Right Hippocampus(53) using co

Re: [Freesurfer] Group comparisons

Sorry, couple more questions: 1) I know that QDEC's/mri_glmfit's equivalent in FSL ("randomise") applies the GLM by doing permutations, and so already corrects for multiple comparisons in the process. How similar is this to what Monte-Carlo does (i.e. controlling FWE via repeated simulations) upon

Re: [Freesurfer] extract pial_lgi from v1.thresh labels

On 03/06/2014 10:34 AM, krista kelly wrote: > Hi Doug, > > Maybe I was mistaken. In your previous email when you said "do not > spec --label-thresh", I thought that you were saying not to use that > option and to just use --slabel for the V1.thresh.label. I've done > that using this command: >

Re: [Freesurfer] Group comparisons

On 03/06/2014 10:35 AM, Tudor Popescu wrote: > Sorry, couple more questions: > > 1) I know that QDEC's/mri_glmfit's equivalent in FSL ("randomise") > applies the GLM by doing permutations, and so already corrects for > multiple comparisons in the process. How similar is this to what > Monte-Car

Re: [Freesurfer] freesurfer coordinates question

There is not an easy way. Start by converting the annotation to a segmentation (mri_annotation2label with --seg output). Binarize the label you are interested in (mri_binarize --i annotseg.mgh --match 2021 --o rh-pericalcarine.mgh), then run mri_surfcluster --in rh-pericalcarine.mgh --thmin .5

[Freesurfer] DICOM input format and structure

Hello, I am new to freesurfer. I went through the Wiki and FAQ's but couldn't find information on the format of the input for recon-all. I understand that one of the input files must have a ".dcm" extension. I have a CD which has MRI scanned images.

Re: [Freesurfer] QDEC bad fd number

Just to follow-up, the sd command is an alias for setting the SUBJECTS_DIR environmental variable to the present working directory. Mihaela was able to get rid of the "Bad fd number" error by running the following commands on her ubuntu workstation. It seems like this error is not freesurfer-

Re: [Freesurfer] DICOM input format and structure

They do not have to have a dcm extension. The 180 files represent many slices from a single volume (or multiple volumes). You need to find out which ones are which. One way to do this is to run dcmunpack -src path-to-dicom folder this will look through all the folders and files under path-to-d

Re: [Freesurfer] DICOM input format and structure

Hi Sravan , please post to the list and not to us personally. Thanks! This is just a list of what you (or whoever you are working with acquired), so I don't know what is in there. Probably #2 is what you want, less sure about #4 doug On 03/06/2014 03:34 PM, Mattevada, Sravan wrote: > Hello Do

Re: [Freesurfer] DICOM input format and structure

Thanks Doug I started the #2 and its running. Sorry about the personal e-mail. Thanks Sravan -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Thursday, March 06, 2014 3:02 PM To: Mattevada, Sravan; Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurf

Re: [Freesurfer] Surface area in aparc stats

Hi Doug, Sorry for forgetting to post to the list. The figure attached to this email could illustrate my questions. The blue region in the figure is a cortical parcellation (i.e. precentral) obtained by FreeSurfer. As I understand, the cortical parcellation has its own thickness (maybe 2~3mm