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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 BFISCHL@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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@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 *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 BFISCHL@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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@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 *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 BFISCHL@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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Katherine Andrade *Sent:* Sunday, February 7, 2021 5:22 PM *To:* 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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