Hello, my name is Wan Park and I am working at Columbia University.
After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average.
After that, Start the Process Volume, but it seems that there is a problem when it tries to strip the skull. i receive this message:
Images (brain): /Users/../Volumes/ste/freesurfer/subjects/scott/mri/brain/COR-001.. not found ... strip skull first
So I go to see the logs and I find this:
/Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig... normalizing image... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 3D bias adjustment took 3 minutes and 23 seconds.
Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain
************************************************************ The input file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain If this is incorrect, please exit quickly the program (Ctl-C)
*************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=125 y=148 z=132 r=54 first estimation of the main basin volume: 693155 voxels
******************************************************** ******************************************************** ******************************************************** White matter intensity 0 is lower than CSF intensity 26. Please examine input images. Will terminate ... ******************************************************** ******************************************************** ********************************************************
************************************************************** MRIstipSkull failed. **************************************************************
Command Finished
Could you tell me what's wrong? Thanks,
Wan Park
Hi Wan,
check the T1 volume and see if it looks correct (the intensity of the white matter should be close to or equal to 110 everywhere pretty much). Also, look at the talairach.xfm with tmedit->file->load transform for main volume and make sure it looks reasonable.
Bruce
On Fri, 20 Aug 2004, Wan Park wrote:
Hello, my name is Wan Park and I am working at Columbia University.
After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average.
After that, Start the Process Volume, but it seems that there is a problem when it tries to strip the skull. i receive this message:
Images (brain): /Users/../Volumes/ste/freesurfer/subjects/scott/mri/brain/COR-001.. not found ... strip skull first
So I go to see the logs and I find this:
/Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig... normalizing image... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 3D bias adjustment took 3 minutes and 23 seconds.
Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain
The input file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain If this is incorrect, please exit quickly the program (Ctl-C)
*************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=125 y=148 z=132 r=54 first estimation of the main basin volume: 693155 voxels
White matter intensity 0 is lower than CSF intensity 26. Please examine input images. Will terminate ...
MRIstipSkull failed.
Command Finished
Could you tell me what's wrong? Thanks,
Wan Park
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
I am using Readhat Enterprise WS 3 on an AMD 64-bit machine. Here is my info: %cat /etc/redhat-release Red Hat Enterprise Linux WS release 3 (Taroon Update 2) %uname -m x86_64
Therefore, I downloaded freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3-full.tar.gz. http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3-full.tar.gz
When I tried to untar the file like: %tar tzf freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3-full.tar.gz http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3-full.tar.gz
I got the error message: ........ freesurfer/bin/mkxsubjreg freesurfer/bin/mris_annot_to_segmentation tar: Skipping to next header tar: Archive contains obsolescent base-64 headers
gzip: stdin: invalid compressed data--crc error
gzip: stdin: invalid compressed data--length error tar: Child returned status 1 tar: Error exit delayed from previous errors
The installation stopped. Anyone has the same kind of problem?
I downloaded the file in Windows sysem and then ftp it to my linux station. Does this matter? Or I need to download another file?
Thank you in advance.
XJ Kang
After the file is downloaded, you can confirm its integrity by checking against the md5sum number for the file shown in the table on the download page at:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
I suspect the file was corrupted somewhere in the download/transfer.
On Tue, 2006-09-26 at 10:49 -0700, XJ Kang wrote:
Hi,
I am using Readhat Enterprise WS 3 on an AMD 64-bit machine. Here is my info: %cat /etc/redhat-release Red Hat Enterprise Linux WS release 3 (Taroon Update 2) %uname -m x86_64
Therefore, I downloaded freesurfer-Linux-centos4_x86_64-stable-pub- v3.0.3-full.tar.gz.
When I tried to untar the file like: %tar tzf freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3-full.tar.gz
I got the error message: ........ freesurfer/bin/mkxsubjreg freesurfer/bin/mris_annot_to_segmentation tar: Skipping to next header tar: Archive contains obsolescent base-64 headers
gzip: stdin: invalid compressed data--crc error
gzip: stdin: invalid compressed data--length error tar: Child returned status 1 tar: Error exit delayed from previous errors
The installation stopped. Anyone has the same kind of problem?
I downloaded the file in Windows sysem and then ftp it to my linux station. Does this matter? Or I need to download another file?
Thank you in advance.
XJ Kang
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Nick Schmansky -
Wan Park -
XJ Kang