Re: [Freesurfer] WMPARC fsaverage

ttle or no scientific value > > > > > > On 9/24/15 6:25 PM, Mohammed Goryawala wrote: > > ​ Hello FreeSurfer Experts, > > This question has been asked before by someone and I am looking to do > something similar. > > ​*If this isn't possible, could we o

[Freesurfer] WMPARC fsaverage

o get wmparc.mgz* *I am also wondering if there is a way to get wmparc.mgz for the fsaverage subject.* *Thanks* *Mohammed Goryawala, PhD* *University of Miami,* *Department of Radiology* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Read .mgz file matlab

(fspec,[],[],headeronly); Error in corticalGMConnectivityMatrixFreeSurfer (line 6) mri = MRIread(MRI_Filename); Thanks Mohammed Goryawala, PhD University of Miami ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

[Freesurfer] Mask T1 Image Cortex

Hello FreeSurfer Experts, I want to zero out all those voxels from my T1 MRI which are not part of the cortex preferably in the native space. I have run the recon-all on the subject. Any help will be great. Thanks Mohammed Goryawala, PhD University of Miami Miller School of Medicine

Re: [Freesurfer] Sulcal CSF Volume

Thanks On Thu, Oct 23, 2014 at 12:34 PM, Douglas N Greve wrote: > > In theory that works, but remember the FS total cranial volume is only > an estimate based on the talairach transform. It is not counting voxels > that are inside the skull. > > On 10/23/2014 12:30 PM, Mohamm

Re: [Freesurfer] Sulcal CSF Volume

like the sulcal CSF. > > doug > > > On 10/22/2014 04:50 PM, Mohammed Goryawala wrote: > > Hello FreeSurfer Experts, > > > > Is it possible to estimate the sulcal CSF volume in Freesurfer > > processing? If not directly are there any indirect means that c

[Freesurfer] Sulcal CSF Volume

Hello FreeSurfer Experts, Is it possible to estimate the sulcal CSF volume in Freesurfer processing? If not directly are there any indirect means that can give me an estimate? Thank you Mohammed Goryawala, PhD Department of Radiology Miller School of Medicine, University of Miami

[Freesurfer] Displaying labels in FreeView

Hello All, I am doing a study and I have determined some regionals volumes in the Aparc and Aseg files which are significant. I would like to show these in Freeview while hiding the other insignificant ones. Please advice if its possible in Freeview. Thank you Mohammed Goryawala, PhD

Re: [Freesurfer] Left and Right Vessels

ely. They could also be lacunae and > not vessels. > > cheers > Bruce > > > > On Tue, 19 Aug 2014, Mohammed Goryawala wrote: > > Hello Freesurfer experts, >> >> In a study I found significant differences in the volume of the left and >> right vesse

[Freesurfer] Left and Right Vessels

Hello Freesurfer experts, In a study I found significant differences in the volume of the left and right vessels of the freesurfer atlas. I wanted to know what regions are included in that ROI and if there are any known functions of these regions. Thank you Mohammed Goryawala, PhD Miller

Re: [Freesurfer] QDEC Cluster Analysis

Thanks Doug. On Aug 1, 2014 4:16 PM, "Douglas N Greve" wrote: > > On 07/31/2014 03:16 PM, Mohammed Goryawala wrote: > > Hello All, > > > > I have some questions related to the qdec analysis I have run. > > > > 1. On running the qdec I see t

[Freesurfer] QDEC Cluster Analysis

completion of the qdec analysis I want to export the clusters created by the qdec analysis into a volumetric file (which I can later convert to .nii). Please also suggest a way that would let me only export clusters above a particular size threshold. Thank you very much in advance. Mohammed Goryawala

Re: [Freesurfer] QDEC Error loading the data table

files? If you created them under windows, then that could be the > problem. If not, post your qdec.table.dat file and the gender.level file > and I'll take a look > > On 06/23/2014 01:33 PM, Mohammed Goryawala wrote: > > Hello FreeSurfer Experts, > > > > I am trying

[Freesurfer] QDEC Error loading the data table

the valid factor names one per line. Error loading the data table. As you see I have a 'gender.levels' file in the same directory as the data file and it reads it above. I still get the error. I am new to QDEC and any help w

Re: [Freesurfer] Tumor Segmentation in FreeSurfer

gt; cheers > Bruce > > > On Wed, 23 Apr > 2014, Mohammed Goryawala wrote: > > > Hello, > > > > I am reposting this question since I have not received any feedback with > > this issue. > > > > I am interested in understanding if tumor segmenta

[Freesurfer] Tumor Segmentation in FreeSurfer

Hello, I am reposting this question since I have not received any feedback with this issue. I am interested in understanding if tumor segmentation can be carried out using FreeSurfer. On examining the stats file we do see a tumor volume reported. I was wondering how this is calculated. Thanks Mo

[Freesurfer] Tumor Segmentation in FreeSurfer

Hello FreeSurfer Experts, On review of stats file in FreeSurfer a tumor volume is reported. How is tumor segmentation achieved by FreeSurfer? Thank you Mohammed Goryawala, PhD ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] ICV

Hi, A follow up question pertaining to this issue for me is how good is the measure of the ICV when dealing with subjects having prior resections or significant atrophy. I am using FreeSurfer v5.1. Thank you M. Goryawala Post-Doctoral Associate Florida International University Miami, FL On Wed

[Freesurfer] Export wmparc to table

Hello FreeSurfer experts, I want to export the white matter volumes from the wmparc stats file to a table. I cannot find the information on the wiki page. Thanks for your help. Dr. Mohammed Goryawala Center for Advanced Technology and Education Miami, Florida

[Freesurfer] qdec Error

such file or directory Please let me know a solution to fix this issue. Thank you for all you help. Mohammed Goryawala ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information