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30132 discussions

Freesurfer stats into REDCap
by Scott Burns 10 Jul '13

10 Jul '13

Hey all, I want to announce a little tool I've been working on. I wanted to be able to put Freesurfer stats into our REDCap databases so our group can more easily analyze these measures against behavioral data. I wrote a tiny little python package that you can find at github.com/sburns/recon-stats to do just that. Hope at least someone else out there can find this useful! Scott Burns Sr. Research Imaging Specialist Education and Brain Science Research Laboratory Vanderbilt University Nashville, TN

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Fwd: wm surf error
by Jason Tourville 10 Jul '13

10 Jul '13

Hello freesurfers, In the attached pic, the red cross hairs fall in the calcarine fissure (right hemisphere). In this scan (and some others I've reviewed recently), this cortex falls within the wm surface and is therefore excluded from the cortical surface. This is despite that area not being labeled as white matter in the wm.mgz volume. It's also despite my efforts to creatively erase wm volume voxels to encourage the wm surface to exclude these cortical voxels. Is there a fix for this type of error? The data were generated with FS v5.3. No control points were set. Thanks for any help, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755 -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

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(no subject)
by Shani Ben Amitay 10 Jul '13

10 Jul '13

Hello freesurfers I'm trying to reconstruct the pial and white surfaces of the rat. The input image is an inverted T2 (attached) and the segmentation to white and gray matter is done using an in house tool. using the following I'm trying to extract the surfaces: mri_fill -CV 120 128 89 -PV 124 137 111 -PV 123 133 113 -PV 123 136 110 -PV123 134 117 mri/white.mgz mri/filled/filled.mgz mri_pretess mri/filled/filled.mgz 255 mri/brain.mgz mri/filled-pretess255. mgz mri_tessellate mri/filled-pretess255.mgz 255 surf/lh.orig.nofix mris_extract_main_component surf/lh.orig.nofix surf/lh.orig.nofix mris_smooth -nw surf/lh.orig.nofix surf/lh.smoothwm.nofix mris_inflate -no-save-sulc surf/lh.smoothwm.nofix surf/lh.inflated.nofix mris_make_surfaces -noaparc -noaseg -mgz -T1 brain ratT1 lh -pial the white surface(red) is ok, the pial surface(yellow) not at all. Any idea if it's possible to fix it? is it possible to give the gray matter segmentation as an initial guess? Thanks ! Shani

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limited number of variables in qdec.table.dat?
by Mürner-Lavanchy, Ines 10 Jul '13

10 Jul '13

Dear experts, is there a limitation concerning the number of variables in qdec (in qdec.table.dat)? I obtained different results when I included about 30 variables vs. only 10 variables in qdec.table.dat for exactly the same analysis, involving only 2 of the variables (I did not include the other variables as nuisance or covariates). I thought there was no influence of the variables I choose for qdec.table.dat, as long as I don't include them in the analysis in qdec. I suppose I'm wrong there? Thank you very much for your help, Ines

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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

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longitudinal processing versioning
by Harms, Michael 09 Jul '13

09 Jul '13

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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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