HI Bruce and freesurfers I have a question about the input file of recon-all I follow the tutorial, first use unpacksdcmdir to convert the original dcm file to a mgz file,then use the recon-all command with the mgz file as the input. I also tried to run the recon-all command with the original dcm file as the input. And I compare the output *.stats files with different inputs, the *.stats files I compared located in <subjectname>/stats/ Then I found a strange thing, the aseg.stats file between the two inputs is the same, however, the aparc file is different,and the difference in some index is larger than we thought. So, I am not sure, which input file is OK for recon-all analysis? I have attached the related results. The version we use is freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0 Thanks for your help! ps1, we use siemens machine, so I put *.IMA as the dcm input ps2, the scanning orient we use is sagittal, however, my partner has asked this question and was answered that we need't reorient it.
Sincerely, Jin
2010-03-03
liyuanyuan60
v4.3.0 has some randomness in its algorithms which account for these differences. if you want the results to repeat from run to run, add the -norandomness flag, or use v4.5.0.
n.
On Wed, 2010-03-03 at 23:27 +0800, liyuanyuan60 wrote:
HI Bruce and freesurfers I have a question about the input file of recon-all I follow the tutorial, first use unpacksdcmdir to convert the original dcm file to a mgz file,then use the recon-all command with the mgz file as the input. I also tried to run the recon-all command with the original dcm file as the input. And I compare the output *.stats files with different inputs, the *.stats files I compared located in <subjectname>/stats/ Then I found a strange thing, the aseg.stats file between the two inputs is the same, however, the aparc file is different，and the difference in some index is larger than we thought. So, I am not sure, which input file is OK for recon-all analysis? I have attached the related results. The version we use is freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0 Thanks for your help! ps1, we use siemens machine, so I put *.IMA as the dcm input ps2, the scanning orient we use is sagittal, however, my partner has asked this question and was answered that we need't reorient it.
Sincerely, Jin
2010-03-03
liyuanyuan60 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Too much thanks for your reply! I will try the 4.5.0 version Best wishes! 2010-03-05
liyuanyuan60
发件人： Nick Schmansky 发送时间： 2010-03-04 22:00:21 收件人： liyuanyuan60 抄送： Freesurfer 主题： Re: [Freesurfer] the input file of recon-all
v4.3.0 has some randomness in its algorithms which account for these differences. if you want the results to repeat from run to run, add the -norandomness flag, or use v4.5.0. n. On Wed, 2010-03-03 at 23:27 +0800, liyuanyuan60 wrote:
HI Bruce and freesurfers I have a question about the input file of recon-all I follow the tutorial, first use unpacksdcmdir to convert the original dcm file to a mgz file,then use the recon-all command with the mgz file as the input. I also tried to run the recon-all command with the original dcm file as the input. And I compare the output *.stats files with different inputs, the *.stats files I compared located in <subjectname>/stats/ Then I found a strange thing, the aseg.stats file between the two inputs is the same, however, the aparc file is different，and the difference in some index is larger than we thought. So, I am not sure, which input file is OK for recon-all analysis? I have attached the related results. The version we use is freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0 Thanks for your help! ps1, we use siemens machine, so I put *.IMA as the dcm input ps2, the scanning orient we use is sagittal, however, my partner has asked this question and was answered that we need't reorient it.
Sincerely, Jin
2010-03-03
liyuanyuan60 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Nick Schmansky