[Freesurfer] Error: cannot determine file type

Hi all, Am receiving the below error, I haven't used this scan before but have never had issues with .dcm. Sorry I'm not sure what sort of scanner they are from. Any help would be appreciated. Cheers, Will /usr/local/freesurfer/subjects/YU mri_convert /home/will/Dropbox/BrainformLtd/Freesurfer

Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl)

urfer support list Message-ID: Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Will can you take the same images with freeview and send them along? Also: tell us a bit about your images. What format did they start in? Were they dicoms? Bruce On Mon, 25 Jan 2016, will b

[Freesurfer] The influence of cortical talairach on final surfaces

Hi all, In the freesurfer pipeline, is cortical segmentation (and the subsequent surface construction) based on the actual scans or on the scan in talairach space? Thanks, Will Brown ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] Cortical gray matter surface area

Hi all, I am a little unclear as to how to find the cortical grey matter volume in the stats output files. The ?.aparc.stats file shows: Measure Cortex, WhiteSurfArea, White Surface Total Area, , mm^2 What about grey? Thanks, Will ___ Freesurfer m

Re: [Freesurfer] Cortical gray matter surface area

g On 8/26/14 8:43 PM, will brown wrote: > Hi all, > > I am a little unclear as to how to find the cortical grey matter > volume in the stats output files. The ?.aparc.stats file shows: > > Measure Cortex, WhiteSurfArea, White Surface Total Area, , mm^2 >

[Freesurfer] Cortical gray matter surface area

Hi all, I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info. ?.aparc.stats reports: Measure Cortex, WhiteSurfArea, White Surface Total Area, , mm^2 How abou

Re: [Freesurfer] Cortical gray matter surface area

You may call it > whatever you'd like) > > > > Just remeber to leave the specified dirs when creating the tables. If you > dont't I think they will be created in the current dir. > > I use FS 5.0. > > Is this what you want? > > > Best, > Andreia &g

Re: [Freesurfer] Cortical gray matter surface area

On Tue, Sep 9, 2014 at 5:36 PM, will brown wrote: > Thanks very much Andreia, yes this does look like what I want. I haven't > had a chance to test it yet but it does indeed appear to answer my > question. Thanks to those that have offered answers, to clarify, I did > indeed mean

Re: [Freesurfer] Cortical gray matter surface area

; hemisphere surface area. > > > Someone from Freesurfer staff will correct me if I'm wrong. (Please) I'm > Ccing Doug since he was replying to your previous emails. > > Let's wait for their feedback. > > Andreia > > > > > Citando will brown : &g

Re: [Freesurfer] Cortical gray matter surface area

Sure. We'd like to know how to find the surface area of the cortical grey matter from the pial surface. So specifically, what is the surface area of the pial/grey matter boundary of the cortex for each hemisphere? We're using Freesurfer v5.3 on Centos 6. Thanks, Will Brown On Fri, Se

Re: [Freesurfer] Cortical gray matter surface area

ot; fields in the output stats/lh.aparc.pial.stats will > be measures of the pial surface as will the SurfArea, MeanCurv, GausCurv, > FoldInd, and CurvInd fields for each ROI (thickness and number of vertices > will stay the same) > > doug > > On 09/11/2014 07:29 PM, will brown

[Freesurfer] CentOs 7

Hi, Is Freesurfer compatible with CentOs 7? Thanks, Will Brown ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to

Re: [Freesurfer] Centos 7

Hi Zeke, I have completed a recon on CentOS 7. As far as I can see, the output matches the results from my previous recon of this subject using Freesurfer on CentOs 6. Is there any particular log that you would like to see? Will ___ Freesurfer mailing l

[Freesurfer] using T2 or flair images

nd stats. Presumably series 1 is the T1 series? Should I use T2 also? if so which one and how? Please excuse my ignorance. Thanks, Will Brown ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurf

[Freesurfer] inverted dicoms

Hi all, I have files that are 2D axial slices that are left-right inverted, so the left side of the brain is on the right side of each slice. Do I need to do anything to the dicoms before importing them into freesurfer? Thanks, Will ___ Freesurfer maili

[Freesurfer] mritotal failed

Hi there, I am receiving the following error during recon-all: mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.7573/src.mnc transforms/talairach.auto.xfm Can't locate shellwords.pl in @INC (@INC contains: /usr/

[Freesurfer] Data requirements

Hi all, I have structural data that has a slice thickness of 5mm and spacing between slices of 5mm (there are around 30 dicom images). I ran it through recon-all but the output was bad. Is it possible to create surfaces from such data? Or is the bad output the answer to this question... Thanks, W

[Freesurfer] Dicom from CT

Hi all, I only have experience processing dicom images from MRI. Can Freesurfer handle images from CT as well? Anything to note? Thanks, Will ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fr

Re: [Freesurfer] Dicom from CT

edu> Content-Type: text/plain; charset=windows-1252; format=flowed What do you mean by "handle"? You cannot run it through the anatomical analysis if that is what you mean. doug On 12/05/2014 03:38 PM, will brown wrote: > Hi all, > > I only have experience processing d