Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

Re: [Freesurfer] New Freesurfer v5.2
by Ed Gronenschild 04 Mar '13

04 Mar '13

Hi Nick, Congratulations and thank you and the whole team (the Freesurfites) very much for your efforts. Cheers, Ed On 03 Mar, 2013, at 18:00, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Freesurfers, > > At long last, a new version of Freesurfer is available for download! > > For a list of what it contains, see this page: > > http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes > > To download it, see this page: > > http://surfer.nmr.mgh.harvard.edu/fswiki/Download > > And remember our home page is here: > > http://surfer.nmr.mgh.harvard.edu > > Our advice concerning your data and different freesurfer versions > is the > same: do not mix versions when processing a set of subjects in your > project. > > The v5.2 default stream (recon-all -all) does not produce > significantly > different results from the v5.1 stream, so there is no compelling > reason > to re-run the default stream on your subject data. However, v5.2 > contains quite a few new features and atlases, which you can run on > data > processed by v5.1. See ReleaseNotes page for details or email the > list: > > http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > Thank you to everyone who downloaded and tested the beta release of > v5.2. > > The Freesurfites > > > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 109, Issue 3 > ****************************************** > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. >

1 0

gcut problem
by Isabelle Deschamps 04 Mar '13

04 Mar '13

Good morning, I tried to run the following command: recon-all -skullstrip -clean-bm -gcut -subjid S01 to remove the skull and remaining dura mater. However, for some subjects, I get the following error: ** Gcutted brain is much smaller than the mask! ** Using the mask as the output instead! I tried adjusting the wsthresh, as suggested in previous posts, but without success. Is there something else, I can try? Thank you in advance for your help, Isabelle

2 1

--tablefile FILE error
by Varghese Chikku 04 Mar '13

04 Mar '13

Dear all, I am getting and error when trying this command, asegstats2table -s truetest1 truetest2 \ --segno 11 12 17 18 \ --tablefile FILE aseg.vol.table ERROR: output table name should be specified (use --tablefile FILE) child process exited abnormally command.I tried using Any Help Chikku

2 1

flatmap of the occipital lobe in fsaverage space
by Andreas Werner 04 Mar '13

04 Mar '13

2 1

Preprocessing anatomical scans
by Isabelle Deschamps 04 Mar '13

04 Mar '13

Dear FS experts, I have multiple anatomical scans acquired on a 3T Philips scanner. The image quality is not the greatest and when I used recon-all –autorecon1 to remove the skull, I noticed that for many scans, the algorithm was not able to find the boundary between the brain and the skull. I tried to adjust the parameters of the mri_watershed to solve the problem, but it did not work. I was wondering if there was a program that I could use to preprocess the anatomical scans, to help with the skull stripping. Thank you, Isabelle

1 0

QDEC - organization of folders for different projects
by Katharina Wittfeld 04 Mar '13

04 Mar '13

Dear FreeSurfer users, we started to analyze structural MRI data from two large cohorts (one with over 2100 and the other with over 1100 subjects). Preprocessing is completely done for all datasets and I've worked myself through this Qdec tutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis) Everthing works fine but I would like to organize the output of qdec project-wise and not all together in the qdec folder in the subject directory. This is important because the qdec.table.dat file would be quite different for the various projects. Is there a way to organize the output like this: /project_1/analysis_1 ... /project_1/analysis_n /project_2/analysis_1 ... /project_2/analysis_n ... and the corresponding qdec.table.dat file in the project_x folder? I tried to run qdec with a qdec.table.dat file saved in another folder but the output is still saved in the subjects dir qdec folder. I would be very grateful for any hint or comment on this topic. Thank you in advance! Best regards, Katharina

2 2

Hippocampus volume calculations
by Garikoitz Lerma-Usabiaga 03 Mar '13

03 Mar '13

Hi, I am calculating hippocampus volumes with 5.2 in CentOS 4. I compare volumes (the same apply for lh and for rh) when calculating as: > Left.Hippocampus value in 1mm3 from aseg.stats > I use the method kvlQuantifyHippocampalSubfieldSegmentations.sh and obtain the nonPartialVolumeStatsLeft.txt, divide each value by 8 in order to get mm3, and sum every column except left_hippocampal_fissure. I obtain quite different values, for example: row.names lh.aseg lhHIP rh.aseg rhHIP 1S_00 4848.83828.187 4878.83767.7392 S_02 4153.83371.517 4547.63389.918 Am I doing anything wrong? Should I calculate the hippos subfields volumes differently? Many thanks! Gari

4 6

New Freesurfer v5.2
by Nick Schmansky 03 Mar '13

03 Mar '13

Freesurfers, At long last, a new version of Freesurfer is available for download! For a list of what it contains, see this page: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes To download it, see this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Download And remember our home page is here: http://surfer.nmr.mgh.harvard.edu Our advice concerning your data and different freesurfer versions is the same: do not mix versions when processing a set of subjects in your project. The v5.2 default stream (recon-all -all) does not produce significantly different results from the v5.1 stream, so there is no compelling reason to re-run the default stream on your subject data. However, v5.2 contains quite a few new features and atlases, which you can run on data processed by v5.1. See ReleaseNotes page for details or email the list: http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Thank you to everyone who downloaded and tested the beta release of v5.2. The Freesurfites

2 1

Re: [Freesurfer] mris_preproc question
by stdp82＠virgilio.it 02 Mar '13

02 Mar '13

I apologize for my question but I have MD background. Can you explain me more basically about permision? Thanks for your kindness and patience Stefano ---Messaggio originale--- Da: greve(a)nmr.mgh.harvard.edu Data: 2-mar-2013 17.08 A: <freesurfer(a)nmr.mgh.harvard.edu> Oggetto: Re: [Freesurfer] mris_preproc question Stefano, you don't have write permission into /Applications/freesurfer/subjects. Give yourself write permissions or use another folder. Another folder is probably better. doug On 3/2/13 5:10 AM, stdp82(a)virgilio.it wrote: > Hi list, > > I'm trying to run mris_preproc. > > I have my recon-all output in > /Application/freesurfer/subjects/subject_prova/folder_for_each_subj > > The file.fsgd is in /Application/freesurfer/subjects directory and it > is called as prova.fsgd. > > When I run: > > mris_preproc --fsgd /Applications/freesurfer/subjects/prova.fsgd > --target fsaverage --hemi lh \ --meas thickness --out > /Applications/freesurfer/subjects/lh.thickness.00.mgh > > I obtain: > > nsubjects = 37 > tmpdir is /Applications/freesurfer/subjects/tmp.mris_preproc.3476 > /Applications/freesurfer/subjects > mkdir: /Applications/freesurfer/subjects/tmp.mris_preproc.3476: > Permission denied > ERROR: creating /Applications/freesurfer/subjects/tmp.mris_preproc.3476 > > To check it, I also attacked the .fsgd file. > > > Thank you very much, > > > Stefano > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

2 1

mris_preproc question
by stdp82＠virgilio.it 02 Mar '13

02 Mar '13

Hi list, I'm trying to run mris_preproc. I have my recon-all output in /Application/freesurfer/subjects/subject_prova/folder_for_each_subj The file.fsgd is in /Application/freesurfer/subjects directory and it is called as prova.fsgd. When I run: mris_preproc --fsgd /Applications/freesurfer/subjects/prova.fsgd --target fsaverage --hemi lh \ --meas thickness --out /Applications/freesurfer/subjects/lh.thickness.00.mgh I obtain: nsubjects = 37tmpdir is /Applications/freesurfer/subjects/tmp.mris_preproc.3476/Applications/freesurfer/subjectsmkdir: /Applications/freesurfer/subjects/tmp.mris_preproc.3476: Permission deniedERROR: creating /Applications/freesurfer/subjects/tmp.mris_preproc.3476 To check it, I also attacked the .fsgd file. Thank you very much, Stefano

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Freesurfer March 2013