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Dear Douglas,
Thank you for your reply.
Could you possibly elaborate more on how this method will only reflect the registration in that area instead of volume? I got this method from freesurfer tutorial on obtaining custom anatomical ROI analysis. And do you have any suggestion on an alternative method to accurately obtain sub thalamic nucleus volume?
Best wishes, Tanrada
On 5 Apr 2021, at 17:00, freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu wrote:
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Today's Topics:
1. Dicom Tag Problem Reconall (Banu Femir) 2. mri_vol2surf empty output (Karan Desai) 3. mri_gtmpvc error Checking tissue type ERROR: CheckSegTissueType() tissue type for seg (Bahar Hazal Yal??nkaya) 4. Re: make_average_subject error (Douglas N. Greve) 5. Re: Running recon-all with FLAIR (Douglas N. Greve) 6. Re: functional to anatomical registration question (Douglas N. Greve) 7. Re: Problem with freesurfer measures (Douglas N. Greve) 8. Re: ERROR: Cannot find stats file (Douglas N. Greve) 9. Re: Subthalamic nucleus volume (Douglas N. Greve) 10. Re: Talairach Failed: Distorted T1 (Douglas N. Greve) 11. Re: quantification of volume of perivascular spaces (Douglas N. Greve) 12. "ERROR: crypt() returned null with 4-line file" (Cook, Philip) 13. Re: Problem with freesurfer measures (Alberto Del Cerro Leon)
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Message: 1 Date: Sun, 4 Apr 2021 22:57:57 +0300 From: Banu Femir banu.femir@gmail.com Subject: [Freesurfer] Dicom Tag Problem Reconall To: freesurfer@nmr.mgh.harvard.edu Message-ID: CANuRgTpGaqjYJVd9V+n3-82ASsx0uP=S=3dH5ksxoxda34S3gA@mail.gmail.com Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Dear Freesurfer Developers,
I'm trying to analyze a set of MRI data that I got via CD. Dicom files did not have .dcm extension, so I used a program and they turned into a .dcm image.
My reconall run for around 2 hours, after I got an error:
Counting frames nframes = 481 nslices = 1 ndcmfiles = 481 PE Dir = UNKNOWN (dicom read) Loading pixel data JPEG compressed, decompressing cd /home/banu/usr/local/freesurfer/subjects/sepsis1dicomwritebelow fsdcmdecompress --i /home/banu/Documents/Sepsis/yeni_dicom_write_below/F_000001.dcm --o /tmp/banu.tmp.decompressed.dcm.1TXZUy --jpeg >& /tmp/banu.tmp.decompressed.dcm.1TXZUy.dcmdjpeg.out ERROR: 512, see /tmp/banu.tmp.decompressed.dcm.1TXZUy.dcmdjpeg.out for more details Linux banuf 4.15.0-51-generic #55-Ubuntu SMP Wed May 15 14:27:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
Before that, I got many Warnings about imagenumber, tag serial number, seriesnumber, tag, ect. In case you want I can share the whole log file. I am wondering if there was sth wrong with my .dcm format. If yes, how I can solve this problem? It seems like there was sth wrong with tags, but I really cannot solve the problem.
Many thanks! Have a nice and healthy week! Banu