[Freesurfer] QDEC Error in Analysis

Hi, I'm a new user of qdec and I'm trying to run a cortical thickness analysis in qdec between Schizophrenic patients and healthy controls. I have run "recon-all -i" and "recon-all -s -qcache" on my data and it says that this has run successfully without any errors. But when I hit analyze on the

[Freesurfer] ERROR: bits = 0 not supported

Hi, I am preprocessing my fMRI data acquired with Philips. when I using the command 'dcmunpack -src . -targ sess01 -run 101 bold nii f.nii .' The error occurred likes below: Found 31 total files. Found 12 unique series: 0 101 301 401 501 601 701 801 901 1001 1101 1201 Subject xxx Date xxx Time

[Freesurfer] CT DIOCMs

Dear Freesurfer experts, I have T1 images acquired using CT scan not MRI. I have the following questions please: 1. "mri_convert" failed to convert the dicoms to nifti, so I used "dcm2nii" part of mricron to convert the dicoms to nifti. I am wondering if there are any tools in Freesurfer to conv

Re: [Freesurfer] mri_normalize problem normalization2

sure, send me the input to mri_normalize and I'll fix it On Wed, 28 Jun 2017, Chris Adamson wrote: Hello,   For one subject I’m getting a weird error on mri_normalize in normalization2. When it goes into the “3d normalization pass 1 of 2” I get an error HISTOalloc(-2147383648): could not a

[Freesurfer] Qdec input fields

Hi, We like using Qdec to display cortical thickness results. The only drawback is that we are unable to manually input values into the boxes for threshold values, FDR rate, etc.. We are running Centos7. We thought the graphics drivers were the problem, but even after buying a whole new GFX car

Re: [Freesurfer] Qdec input fields

Sorry, qdec has been slowly losing functionality because no one here is maintaining it. Its a deprecated tool and we frequently do get reports of users being unable to manually input values into the boxes. Very odd indeed that your colleague can SSH into it and bypass the problem. Unfortunately

[Freesurfer] mri_glmfit error (mri_reshape number of elements)

Hi, I’m running a group-level analysis and have encountered an error that results in a core dump. The first-level analyses were run using the fsaverage surfaces, rather than self surfaces. I’ve already inspected the individual contrasts, loading the fsaverage surface in tksurfer and rendering ea

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

Dear Dr. Yeo, Our research group is currently trying to segment the Yeo atlas into separate labels, but just came across this thread which indicates that you have already done this. Would you be willing to re-share the link to your previously extracted individual labels from your 7 and 17 networks

Re: [Freesurfer] mri_normalize problem normalization2

How can I do that? Can I send it to an email address via a file sender? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, 29 June 2017 12:03 AM To: Freesurfer support list Subject: Re:

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

Hi Corinna, You can download here: https://www.dropbox.com/s/yj1gbpmpgho7wtm/Yeo_JNeurophysiol11_SplitLabels.zip?dl=0 Regards, Thomas On Thu, Jun 29, 2017 at 5:45 AM, Corinna Bauer wrote: > Dear Dr. Yeo, > > Our research group is currently trying to segment the Yeo atlas into > separate label