[Freesurfer] co-registration: SWI images with FLAIR

Dear All, Can I co-register SWI with FLAIR images using Freesurfer? thanks Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and

[Freesurfer] Postdoctoral Fellow (neuroimaging) in Aging

Postdoctoral Fellow in Neuroimaging (MRI)/Cognitive Aging Area Cerebrovascular Laboratory Department Institute for Exercise and Environmental Medicine Institution The University of Texas Southwestern Medical Center of Dallas Job Description The applicant should have a Ph.D. and/or M.D. degree. Exp

Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all

Well, I am using version 5.1.0. I have had same issue in fewer subjects when I used the older version as well. Any comments about that? -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Monday, July 16, 2012 3:04 PM To: Ayaz, Muhammad Cc: freesurfer

[Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all

Dear All, After running recon-all, I noticed several subjects that sum of WM and GM is bigger than ICV. I have re-run these subjects and the results is the same sum of GM and WM is coming out to be bigger than ICV. Any suggestions? I need to calculate normalized volumes. Regards Ayaz The inf

[Freesurfer] ICV measurement in freesrufer

Dear all, How does the freesurfer calculate the ICV? By adding up all the cortical and sub-cortical volumes including WM and GM and CSF? If so does it also include cerebellum and brain stem? Thanks Ayaz The information contained in this message and any attachments is intended only for the u

Re: [Freesurfer] total wm volume

voxels (actually, there is some partial volume correction too), so the values will not add up perfectly. doug On 4/2/12 9:22 AM, Ayaz, Muhammad wrote: Dear All, I used the following command line to extract the volumes from Stats file. asegstats2table --subjects sub1 sub2... --stats wmparc.stats

[Freesurfer] total wm volume

Dear All, I used the following command line to extract the volumes from Stats file. asegstats2table --subjects sub1 sub2... --stats wmparc.stats --tablefile aseg_wm_volume.txt ?h.CorticalWhiteMatterVol generated using the above command does not match the volume which I calculated by adding al

[Freesurfer] DTI analysis: freesurfer vs DTI studio

Dear All, I am new to freesurfer DTI analysis. Can anybody explain what is the advantage of using freesurfer for DTI analysis over DTI studio? Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed,

Re: [Freesurfer] recon-all and corrected hemispheres

ugust 11, 2011 2:23 PM To: Ayaz, Muhammad Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] recon-all and corrected hemispheres Hi Ayaz the big difference is that once you convert to analyze you will never be sure which side of the image is anatomically on the left and w

Re: [Freesurfer] recon-all and corrected hemispheres

. Should I use par images to transform them into dicom on scanner or is there any other way to do it?. Thanks Ayaz -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, August 11, 2011 2:10 PM To: Ayaz, Muhammad Cc: 'freesurfer@nmr.mgh.harvar

[Freesurfer] recon-all and corrected hemispheres

Dear All, I acquired the images using Phillips scanner. I converted the images from par into analyze using MRIcro. I noticed that images were flipped when I view them in the axial plane, i.e. when I look at the images on the computer screen the Right hemisphere (where we tapped the fish oil tab

[Freesurfer] Phillips 3T

Dear All, I have T1 images single scan from Phillips 3T. Images quality looks good. Since we use 8 channel should I be collecting 2 data set to average or single data will be sufficient? Ayaz The information contained in this message and any attachments is intended only for the use of the in

[Freesurfer] wmparc.stats do not contain ctx colume after recon-all

Dear All, After running recon-all I noticed wmparc.stats only contains wm volume and there is no ctx volume and subcortical volumes. Recon-all finished without any error. Thanks Ayaz The information contained in this message and any attachments is intended only for the use of the individu

[Freesurfer] wmparc.mgz

Dear All, After running recon-all I noticed wmparc.mgz only contains wm volume and there is no ctx volume and subcortical volumes. Recon-all finished without any error. Thanks Ayaz The information contained in this message and any attachments is intended only for the use of the individual or

Re: [Freesurfer] fsaverage error with recon-all

: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Tuesday, May 31, 2011 8:48 AM To: Ayaz, Muhammad Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] fsaverage error with recon-all Hi Ayaz you need to create a symlink to the fsaverage subject we distribute in your SUBJE

[Freesurfer] fsaverage error with recon-all

Dear All, I ran recon-all using single MPRAGE data set. Processing exited with an error pasted below indicating there is not fsaverage. Thanks Ayaz #@# BA Labels lh Fri May 27 21:47:56 CDT 2011 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject...