Hi Doug, Doug, it's very kind of you to help me all the time. Thanks. I didnot do anything except move all DICOM files into one folder which is the same as other subjects. According your prompt, I checked the DICOM and found that this subjects have two 3d imag. And I separated the data into 2 folders. So the recon-all running normally. Thanks Doug. All the best.
2013-12-19
Rujing Zha
发件人：Douglas N Greve greve@nmr.mgh.harvard.edu 发送时间：2013-12-19 04:48 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人："Rujing Zha"charujing123@163.com 抄送："freesurfer"freesurfer@nmr.mgh.harvard.edu
There are lots of warnings in the log file. Have you anonymized this data or done anything to the DICOM files since they came from the scanner?
On 12/18/2013 03:44 AM, Rujing Zha wrote:
Dear Doug, Thanks for your kindhearted help, Doug. I upload the standard output and error message file named "unpack_log", and the unpack log file named unpack.log in the attachment. Thanks in advance. All the best. 2013-12-18
/Rujing Zha/
*发件人：*Douglas N Greve greve@nmr.mgh.harvard.edu *发送时间：*2013-12-18 00:51 *主题：*Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR *收件人：*"Rujing Zha"charujing123@163.com *抄送：*"freesurfer"freesurfer@nmr.mgh.harvard.edu Is that all it says? Can you send the log file? On 12/16/2013 10:00 PM, Rujing Zha wrote:
Hi Doug, Thanks Doug. I tried the "-run 15" option, it generate a "015" folder. However unpacksdcmdir code echo ERROR message: "ERROR:mri_convert child killed: segmentation violation ", and the script terminated. All the best. 2013-12-17
/Rujing Zha/
*发件 人：*Douglas N Greve greve@nmr.mgh.harvard.edu *发送时间：*2013-12-17 02:56 *主 题：*Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR *收件 人：*"freesurfer"freesurfer@nmr.mgh.harvard.edu *抄送：* If you passed "-run 015" it should have generated a 015 folder and not a
013 folder. The only thing I can think may have gone wrong is that it expected 15 instead of 015. doug On 12/16/2013 09:24 AM, Bruce Fischl wrote:
sorry, I don't know that code very well. Doug is probably the right one to help you Bruce
On Mon, 16 Dec 2013, Rujing Zha wrote:
Dear Bruce, I did setup the "-run 015" not "013" in unpacksdcmdir as I told in previous message. But it generated the "013" folder automatically after running
unpacksdcdir, which made me so confused. As it created the "013" folder, I guess unpacksdcmdir didnot recognized
structure image correctly which was in the "15th" line of the scan.info.
Thanks Bruce. All the best.
2013-12-16
Rujing Zha
发 件 人：Bruce Fischl fischl@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:12 主
题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the
command-line ERROR 收件 人："Rujing Zha"charujing123@163.com 抄 送："freesurfer"freesurfer@nmr.mgh.harvard.edu
but why are you giving recon-all the path to run 013 instead of 015? I
don't know the fsfast file structure, but your scan.info says that 013 is
?? ?an EPI fun and 015 is the mprage
On Sat, 14 Dec 2013, Rujing Zha wrote:
Hi Bruce, It generated a 013 subfolder in after running this code "unpacksdcmdir
-src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015
3danat mg z
001.mgz". It is 15 that I can see the number of
t1_mpr_ns_sag_iso_zhang
?? ?in
the unpack.log. Then I ran "recon-all -i ../work/liujunhao/3danat/013/001.mgz -s
liujunha o",
and it finished without error. "recon-all -s liujunhao -all" was run and ERROR would be displayed:
ERROR: input(s) cannot have multiple frames! The recon-all.log unpack.log and scan.info were unloaded in the
attachmen t.
Thanks. All the best.
2013-12-14
Rujing Zha
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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