Hi Katie
I don’t know what iEEGview is. When you run recon-all on dicoms you give it a
*single* file in the correct series and it sorts out the rest of them and will
ignore files from other series in that directory
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Katherine Andrade
Sent: Monday, February 8, 2021 4:26 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Issue with Segmentation
External Email - Use Caution
I see. So when I run the segmentation I should only have the folder that says
DICOM and within just have the MRI folder with dicom format files inside? I was
reading the Manual and it had said the following:
"Before localization, a subject folder should be created. The folder name
should be the subject whose data are going to be analyzed in the following step
(the name set in the panel Configuration). In the subject folder, a folder
called DICOM should be created before running the function of iEEGview, the
DICOM folder should contains two subfolders called MRI and CT, where the MRI
and CT 'dicom' format files are placed. After the correct placing of images
files, brain segmentation and electrodes reconstruction can be realized through
below steps"
Therefore I had the dicoms in each of the folders and then I ran the
segmentation. But if I am understanding you correctly, I should just have the
MRI dicoms and not the CT dicoms in the DICOM folder since iEEGview only
processes MRI and not CT?
-Katie
On Mon, Feb 8, 2021 at 12:25 PM Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote:
Well, we only process MRI, not CT, so definitely don’t give us a CT! And
generally you need a T1-weighted MRI that is about 1mm isotropic
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Katherine Andrade
Sent: Monday, February 8, 2021 3:07 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Issue with Segmentation
External Email - Use Caution
Could you elaborate what you mean by volumes and would I get the volumes
within the recon-all log file I sent your way?
So I am inputting MRI and CT scans that are given to us via DICOMS. I used 3D
slicer to look and see which is the best looking series and then I upload those
dicoms into iEEGview in order to do segmentation-->coregistration--> and then
electrode localization.
Best,
Katie
On Mon, Feb 8, 2021 at 11:05 AM Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Katie
I defer to others for this particular problem, but I would strongly advise
looking at the various volumes recon-all outputted prior to that and make sure
that they are all reasonable-looking. Can you also tell us what your input data
is?
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Katherine Andrade
Sent: Monday, February 8, 2021 1:05 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Issue with Segmentation
External Email - Use Caution
Hi Bruce,
Thank you for your prompt response. We were able to successfully run
segmentation on another dataset that we've received from one University but
when we attempt to run the segmentation from the dataset from another
University, we can't complete segmentation.
This is what Matlab says:
---------------------------------------------------------------------------------------
Checking to see if freesurfer segmentation has started...
Freesurfer segmentation has started; this process may take more than 24 hours...
The progress of the segmentation process can be observed by opening
/home/bdl/freesurfer/subjects/SD06/scripts/recon-all.log
When the segmentation is complete the results are saved in
/home/bdl/freesurfer/subjects/SD06/...The pial surfaces are saved as rh.pial
and lh.pial in SD06/surf/...
Segmentation processing... Please don't turn off your computer!
-----------------------------------------------------------------------------------------
I've attached the recon-all.log below and it mentions there is an Error that
says "don't know how to get DWI parameters from.
Is there anyway you can help me debug this issue. I know this process shouldn't
be taking so long.
Best,
Katie
On Sun, Feb 7, 2021 at 2:38 PM Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Katie
Can you give us more info? What command line did you run? Can you send us the
recon-all.log file from the subject so we can see what step it is on? Usually
this means the topology fixer is trying to fix something giant, like the
cerebellum attached to cortex or skull left around or something
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Katherine Andrade
Sent: Sunday, February 7, 2021 5:22 PM
To: Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Issue with Segmentation
External Email - Use Caution
To whom this may concern,
I've been running segmentation for over 100 hours and I'm not entirely sure
how to fix this issue. Is this the right address to ask for help?
Best,
Katie
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