Freesurfer July 2013

freesurfer@nmr.mgh.harvard.edu

165 participants
332 discussions

Fwd: how to use mris_register?
by fatma zribi 10 Jul '13

10 Jul '13

---------- Forwarded message ---------- From: fatma zribi <zribi.fatma(a)gmail.com> Date: 2013/7/10 Subject: Re: [Freesurfer] how to use mris_register? To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Hi Bruce, Thank you very much for your help but it still don't work. mris_register s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere avg_all_subjects_SD/lh.reg.template.tif lh.sphere_reg $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere... MRISread(s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere): could not open file No such file or directory mris_register: could not read surface file s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere No such file or directory note that the file exist in the folder and i have changed the SUBJECT_DIR to the appropriate folder Thank you very much for your help with best regards, Fatma 2013/7/9 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Fatma > > don't use the -1 flag if you are regtering to a template, only if you are > registering individual surfaces to each other. You probably want the output > to be named lh.sphere_reg and go in the s000/surf dir. > > cheers > Bruce > > > On Tue, 9 Jul 2013, fatma zribi wrote: > > Dear Mr, >> >> When I execute mris_register to register one subject to a template., I >> have this message of error: >> >> mris_register -1 s000/surf/lh.sphere avg_all_subjects_SD/lh.reg.**template.tif >> sphere_reg >> treating target as a single subject's surface... >> $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ >> $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ >> reading surface from s000_open_brain_sanlm_+TIR_** >> normlalized/surf/lh.sphere... >> MRISread(s000_open_brain_**sanlm_+TIR_normlalized/surf/**lh.sphere): >> could not open file >> No such file or directory >> mris_register: could not read surface file s000/surf/lh.sphere >> No such file or directory >> >> note that the file exist in the specifeid SUBJECT_DIR >> >> Thank you for your help >> >> Fatma >> >> >> >> > > 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<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. >

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Error after recon_all on pre-BETed image
by Lin, Richard Lee-Tsong 10 Jul '13

10 Jul '13

Hi FS gurus, For whatever reason, BET worked better on my structural image than mri_watershed, so I used a BET image with recon-all -autorecon1 -noskullstrip. Here is a summary of the codes that I used: bet structural.nii structural_brain.nii.gz recon-all -i structural.nii -s {subjid} recon-all -autorecon1 -noskullstrip -s {subjid} mri_convert structural_brain.nii.gz {FS_directory}/{subjid}/mri/brainmask.mgz recon-all -autorecon2 -autorecon3 -subjid {subjid} Stage 1 ran without errors. Stage 2 ran with errors, but when I checked the log (see attached), and the only message that resembled error to me was the following: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH Is there something I did wrong? Thanks. Best, Richard

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Re: [Freesurfer] how to use mris_register?
by Bruce Fischl 10 Jul '13

10 Jul '13

I mean send your email to the FreeSurfer list as well so that others can answer (which I'll do on this email). Are you sure you don't have a typo in your command line? You typed "normlalized" instead of "normalized" cheers Bruce On Wed, 10 Jul 2013, fatma zribi wrote: > Hi Bruce, > > i didn't understand 'cc' of your message.. > > i try to execute mris_info : mris_info s000_open_brain_sanlm_+TIR_normlalized/surf/lh.curv > MRISread(s000_open_brain_sanlm_+TIR_normlalized/surf/lh.curv): could not open file > No such file or directory > could not open s000_open_brain_sanlm_+TIR_normlalized/surf/lh.curv > > but the folder of the subject exist and the file lh.curv exist too > > I will be very grateful if you accept to help me. > > With best regards, > > Fatma > > > > 2013/7/10 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Fatma > > can you cc the list on these emails? Are you sure the file exists with that exact name? Can you run mris_info on it? > > cheers > Bruce > On Wed, 10 Jul 2013, fatma zribi wrote: > > Hi Bruce, > > Thank you very much for your help but it still don't work. > > mris_register s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere > avg_all_subjects_SD/lh.reg.template.tif lh.sphere_reg > > $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ > $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ > reading surface from s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere... > MRISread(s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere): could not open file > No such file or directory > mris_register: could not read surface file s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere > No such file or directory > > note that the file exist in the folder and i have changed the SUBJECT_DIR to the appropriate folder > > Thank you very much for your help > > with best regards, > > Fatma > > > > 2013/7/9 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Fatma > > don't use the -1 flag if you are regtering to a template, only if you are registering individual > surfaces to each > other. You probably want the output to be named lh.sphere_reg and go in the s000/surf dir. > > cheers > Bruce > > On Tue, 9 Jul 2013, fatma zribi wrote: > > Dear Mr, > > When I execute mris_register to register one subject to a template., I have this message of > error: > > mris_register -1 s000/surf/lh.sphere avg_all_subjects_SD/lh.reg.template.tif sphere_reg > treating target as a single subject's surface... > $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ > $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ > reading surface from s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere... > MRISread(s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere): could not open file > No such file or directory > mris_register: could not read surface file s000/surf/lh.sphere > No such file or directory > > note that the file exist in the specifeid SUBJECT_DIR > > Thank you for your help > > Fatma > > > > > > 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. > > > > > >

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Basic question for running recon-all on ios
by Pascal Bou-Haidar 09 Jul '13

09 Jul '13

Hi Freesurfer users, I am new to Freesurfer and have run into difficulty with running the recon-all command in terminal on osx. When I type in the command bellow recon-all –i IM-0001-0001.dcm –subject bert –all I receive ERROR: Flag i unrecognized. Also the usage info on recon-all does not list -i as far as I can see. Has it been replaced by a different flag? On a different note. Has anyone tried to install freesurfer on a second partition with the drive name containing a space character? I have two drives installed on my mac with the second drive foolishly labeled "Second Drive". When I tried to install the bash script (export and source commands) it ran into trouble recognising the space character between second and drive. I had to change the name to Second_Drive which unfortunately mucks up other apps that use the reference to that original name fine. Any words of wisdom would be greatly appreciated. Thanks in advance Pascal

2 1

longitudinal processing versioning
by Harms, Michael 09 Jul '13

09 Jul '13

2 1

Is it true that wm.mgz should lie inside the boundary of the white matter?
by ye tian 09 Jul '13

09 Jul '13

Dear Freesurfers, I have carefully gone through the tutorial data "good_output", and find that wm.mgz lies inside the boundary of the white matter almost all the time, with fewer than 10 slices of exception. Whenever there is an exception, the affected area is relatively small. Therefore, I am wondering 1) Should wm.mgz always lie inside the boundary of the white matter? 2) If I have subjects whose wm.mgz lies outside the boundary of the white matter (which I do), should I add control points until the two nearly match? Thank you very much! Sincerely, Ye

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Longitudinal processing
by Jonathan Holt 09 Jul '13

09 Jul '13

As I'm having trouble importing nifti files into the first step of the longitudinal work flow, I'm wondering if I can use volumes generated from recon-all -s <subjID> for the second and third steps of the workflow. jon

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Group Analysis
by Nooshin Zadeh 09 Jul '13

09 Jul '13

Dear Freesurfer group I am interested to do group analysis on my data. If I want to do inter-individual group analysis, what is the minimum number of subjects I need to have? Also if I want to do intra-individual analysis, what is the best way in FS? I appreciate your time and your help. Thanks a lot, Nooshin

2 1

(no subject)
by Nicholas Paul Denisuk 09 Jul '13

09 Jul '13

Dear Freesurfer Users, I am trying to regress out the activity associated with button presses in my GLM analysis. How do I generate a nuisance regressor file analogous to a white matter regressor generated in functional connectivity (a one column time course file)? Thanks you, Nick

2 1

Subcortical volume stream
by Jim Monti 09 Jul '13

09 Jul '13

Hello, I would like to verify something regarding subcortical volume estimation in Freesurfer before we move forward with our analyses. From what I've read on the wiki and listserv, it seems the subcortical and cortical processing streams are largely independent. If one were only interested in subcortical volumes (e.g. hippocampus, striatum) is it sufficient to run recon-all -all on the participants, verify/correct any issues with the registration, verify that the segmentations look correct, and then move forward with statistical analyses on the subcortical volumes using aseg.stats, or will refinements in the surfaces (e.g. manually removing dura mater from the pial surface) have an effect on subcortical volume and thus it is necessary to check the surfaces as well, make the corrections, rerun autorecon 2 and 3, the and then perform stats on the subcortical volumes? Thank you in advance for your time. Sincerely, Jim Monti -- Jim Monti PhD Candidate 2012-2013 Beckman Institute Graduate Fellow Memory Systems Laboratory (http://msl.beckman.illinois.edu/) Psychology-Cognitive Neuroscience University of Illinois at Urbana-Champaign

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Freesurfer July 2013