Hi everyone,
I am a new user of freesurfer. As a first step, I wrote a script (see below between ---) to run recon-all on the anatomical data. Since I found it very slow, and our server has multi-cores, I run this script manually several times, thus it appeared to be parallel.Then I have several questions:
1 From the screen output, I guess if a certain subject folder exists, freesurfer will refuse to work on this subject. Then I have assumption that if I run the same script multiple times would not overwrite results from previous session. Can I hold this believe? 2 After certain time, I found new folders with name such as [fsaverage], which I assumed as kind of average of subjects. Then I worry this was generated from one session (either the first one or the last one, depending on overwriting policy of this folder). For example, if session one worked on subject 1 4 7 ... and session two worked on subject 2 5 8... and session three worked on subject 3 6 9 ... ; is this [fsaverage] an average of (subject 1, 4, 7) or (subject 3, 6, 9)? Or I am so lucky that it is the average all processed subjects? 3 Is there a proper way to work in parallel than my stone-age way? 4 I searched the wiki and found some slides and pages which may help but not answering the above question. Would you please suggest an example "full" script of analysis? Thank you very much! ======= My environment: 64-bit Linux with OpenSUSE. 8-CPUs/32G mem Script: ------------- #!/bin/csh echo "beginning ..."
#environment setup source ~/1tests/FreeSurferEnv.csh
#Set environment and get the filelist set raw_dir = '~/2rawdata/' set fileNameList = `ls {$raw_dir}`
#Try all the subjects in a loop foreach file ($fileNameList) echo "Now processing file ($file): ..." echo "" set inName = ($raw_dir$file) recon-all -i $inName -s $file -autorecon-all end
echo "done!" ------------- =======
Hi everyone,
I just re-checked the folder [fsaverage], their modified date was quite old, probably they are just copies from freesurfer installation folder rather than results of my scripts. Then my question 2 become void...
best! Peng
---------- Forwarded message ---------- From: peng prion.w@gmail.com Date: Thu, Feb 6, 2014 at 11:00 AM Subject: A question on fsaverage To: Freesurfer@nmr.mgh.harvard.edu
Hi everyone,
I am a new user of freesurfer. As a first step, I wrote a script (see below between ---) to run recon-all on the anatomical data. Since I found it very slow, and our server has multi-cores, I run this script manually several times, thus it appeared to be parallel.Then I have several questions:
1 From the screen output, I guess if a certain subject folder exists, freesurfer will refuse to work on this subject. Then I have assumption that if I run the same script multiple times would not overwrite results from previous session. Can I hold this believe? 2 After certain time, I found new folders with name such as [fsaverage], which I assumed as kind of average of subjects. Then I worry this was generated from one session (either the first one or the last one, depending on overwriting policy of this folder). For example, if session one worked on subject 1 4 7 ... and session two worked on subject 2 5 8... and session three worked on subject 3 6 9 ... ; is this [fsaverage] an average of (subject 1, 4, 7) or (subject 3, 6, 9)? Or I am so lucky that it is the average all processed subjects? 3 Is there a proper way to work in parallel than my stone-age way? 4 I searched the wiki and found some slides and pages which may help but not answering the above question. Would you please suggest an example "full" script of analysis? Thank you very much! ======= My environment: 64-bit Linux with OpenSUSE. 8-CPUs/32G mem Script: ------------- #!/bin/csh echo "beginning ..."
#environment setup source ~/1tests/FreeSurferEnv.csh
#Set environment and get the filelist set raw_dir = '~/2rawdata/' set fileNameList = `ls {$raw_dir}`
#Try all the subjects in a loop foreach file ($fileNameList) echo "Now processing file ($file): ..." echo "" set inName = ($raw_dir$file) recon-all -i $inName -s $file -autorecon-all end
echo "done!" ------------- =======
Hi Peng
the recon-all instances should be able to be run in parallel. The first time you run one it will see that fsaverage does not exist, and will symlink it to $FREESURFER_HOME/subjects/fsaverage (which is our existing coordinate system, NOT an average of your subjects - to make your own average use the make_average_subject script).
cheers Bruce
On Thu, 6 Feb 2014, peng wrote:
Hi everyone,
I am a new user of freesurfer. As a first step, I wrote a script (see below between ---) to run recon-all on the anatomical data. Since I found it very slow, and our server has multi-cores, I run this script manually several times, thus it appeared to be parallel.Then I have several questions:
1 From the screen output, I guess if a certain subject folder exists, freesurfer will refuse to work on this subject. Then I have assumption that if I run the same script multiple times would not overwrite results from previous session. Can I hold this believe? 2 After certain time, I found new folders with name such as [fsaverage], which I assumed as kind of average of subjects. Then I worry this was generated from one session (either the first one or the last one, depending on overwriting policy of this folder). For example, if session one worked on subject 1 4 7 ... and session two worked on subject 2 5 8... and session three worked on subject 3 6 9 ... ; is this [fsaverage] an average of (subject 1, 4, 7) or (subject 3, 6, 9)? Or I am so lucky that it is the average all processed subjects? 3 Is there a proper way to work in parallel than my stone-age way? 4 I searched the wiki and found some slides and pages which may help but not answering the above question. Would you please suggest an example "full" script of analysis? Thank you very much! ======= My environment: 64-bit Linux with OpenSUSE. 8-CPUs/32G mem Script:
#!/bin/csh echo "beginning ..."
#environment setup source ~/1tests/FreeSurferEnv.csh
#Set environment and get the filelist set raw_dir = '~/2rawdata/' set fileNameList = `ls {$raw_dir}`
#Try all the subjects in a loop foreach file ($fileNameList) echo "Now processing file ($file): ..." echo "" set inName = ($raw_dir$file) recon-all -i $inName -s $file -autorecon-all end
echo "done!"
=======
Bruce, Thanks a lot! Would you explain more on how to run recon-all in parallel? By run the script it did not automatically took the advantage of multiple cores (by checking CPU usage). Is their somewhere I can change the preference or I shall add some parameters in my code?
On Thu, Feb 6, 2014 at 2:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Peng
the recon-all instances should be able to be run in parallel. The first time you run one it will see that fsaverage does not exist, and will symlink it to $FREESURFER_HOME/subjects/fsaverage (which is our existing coordinate system, NOT an average of your subjects - to make your own average use the make_average_subject script).
cheers Bruce
On Thu, 6 Feb 2014, peng wrote:
Hi everyone,
I am a new user of freesurfer. As a first step, I wrote a script (see below between ---) to run recon-all on the anatomical data. Since I found it very slow, and our server has multi-cores, I run this script manually several times, thus it appeared to be parallel.Then I have several questions:
1 From the screen output, I guess if a certain subject folder exists, freesurfer will refuse to work on this subject. Then I have assumption that if I run the same script multiple times would not overwrite results from previous session. Can I hold this believe? 2 After certain time, I found new folders with name such as [fsaverage], which I assumed as kind of average of subjects. Then I worry this was generated from one session (either the first one or the last one, depending on overwriting policy of this folder). For example, if session one worked on subject 1 4 7 ... and session two worked on subject 2 5 8... and session three worked on subject 3 6 9 ... ; is this [fsaverage] an average of (subject 1, 4, 7) or (subject 3, 6, 9)? Or I am so lucky that it is the average all processed subjects? 3 Is there a proper way to work in parallel than my stone-age way? 4 I searched the wiki and found some slides and pages which may help but not answering the above question. Would you please suggest an example "full" script of analysis? Thank you very much! ======= My environment: 64-bit Linux with OpenSUSE. 8-CPUs/32G mem Script:
#!/bin/csh echo "beginning ..."
#environment setup source ~/1tests/FreeSurferEnv.csh
#Set environment and get the filelist set raw_dir = '~/2rawdata/' set fileNameList = `ls {$raw_dir}`
#Try all the subjects in a loop foreach file ($fileNameList) echo "Now processing file ($file): ..." echo "" set inName = ($raw_dir$file) recon-all -i $inName -s $file -autorecon-all end
echo "done!"
=======
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