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mris_curvature_stats
by Harms, Michael 11 Jul '13

11 Jul '13

1 0

bugs with expert-options and clean flags
by Harms, Michael 11 Jul '13

11 Jul '13

1 0

Fwd: How to use read_curv?
by fatma zribi 11 Jul '13

11 Jul '13

---------- Forwarded message ---------- From: fatma zribi <zribi.fatma(a)gmail.com> Date: 2013/7/11 Subject: Re: How to use read_curv? To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> i have used read_surf to read ?h.white data. Now i would like to use curv and sulc file of FreeSurfer and extract the variance compared two one template of the average of 80subjects. We hav'ent a method to go from curv file to plot a mesh with matlab. 2013/7/11 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > sorry, I still don't understand what the issue is. read_surf will give you > the surface geometry/topology, and read_curv will give you the scalar > fields to display over them. You can use mri_surf2surf to map them into a > common space (the fsaverage surface for example) > > > cheers > Bruce > On Thu, 11 Jul 2013, fatma zribi wrote: > > Hi Bruce, >> >> I would like to use information about curv and sulc of a population and >> plot >> the variance with plot_mesh (variance presented in one brain) >> >> With best regards, >> >> Fatma >> >> >> 2013/7/11 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Fatma >> >> I don't understand your question. read_curv returns a scalar >> field over the surface, not the surface itself, which is why it >> is nvertices x 1. Use read_surf to read the surface topology in >> >> cheers >> Bruce >> On Thu, 11 Jul 2013, fatma zribi wrote: >> >> Dear Bruce, >> Now i would like to use the function read_curv but I >> have a problem of >> dimension .. curv is a vector of [143704,1] and >> vertices must be a matrix of >> [3, 143704] >> >> Would you mind help me and send an exemple of the >> use of the function wiht >> the visualisation of the brain >> >> [curv, fnum] = >> read_curv([SD_atlas.parms.**SUBJECTS_DIR '/' >> SD_atlas.parms.SUBJECT '/surf/' SD_atlas.parms.hemi >> '.curv']); >> >> white_sbjMesh.vertices = curv'; >> white_sbjMesh.faces=(fnum+1)'**; >> >> SD_white_remeshed{j}.vertices = >> MARS_linearInterpolate(max_**mesh.vertices, >> SD_sphere_sbjMesh, white_sbjMesh.vertices); >> >> SD_avg_mesh.vertices = >> SD_avg_mesh.vertices+SD_white_**remeshed{j}.vertices; >> >> Thank you very much for your help >> >> with best regards, >> >> 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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How to use read_curv?
by fatma zribi 11 Jul '13

11 Jul '13

Dear Bruce, Now i would like to use the function read_curv but I have a problem of dimension .. curv is a vector of [143704,1] and vertices must be a matrix of [3, 143704] Would you mind help me and send an exemple of the use of the function wiht the visualisation of the brain [curv, fnum] = read_curv([SD_atlas.parms.SUBJECTS_DIR '/' SD_atlas.parms.SUBJECT '/surf/' SD_atlas.parms.hemi '.curv']); white_sbjMesh.vertices = curv'; white_sbjMesh.faces=(fnum+1)'; SD_white_remeshed{j}.vertices = MARS_linearInterpolate(max_mesh.vertices, SD_sphere_sbjMesh, white_sbjMesh.vertices); SD_avg_mesh.vertices = SD_avg_mesh.vertices+SD_white_remeshed{j}.vertices; Thank you very much for your help with best regards, Fatma

2 3

mri_nu_correct.mni
by Anna Josefson 11 Jul '13

11 Jul '13

Hi list, I have been trying to test out bias correction on hi-res post mortem animal MRI data. (which is not going through regular FS analysis pipeline) Is there any option for not changing the resolution ? from mri_nu_correct.mni.log: Original Data has (0.234375, 0.234375, 0.400003) mm size and (384, 384, 137) voxels. Data is conformed to 1 mm size and 256 voxels for all directions. Thanks a lot! Anna

3 2

Fwd: Fwd: how to use mris_register?
by fatma zribi 11 Jul '13

11 Jul '13

---------- Forwarded message ---------- From: fatma zribi <zribi.fatma(a)gmail.com> Date: 2013/7/10 Subject: Re: [Freesurfer] Fwd: how to use mris_register? To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Copie1/s000_open_brain_sanlm_+TIR_normlalized$ ls -l total 704 drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 bem drwxrwxr-x 2 zribi.f scalp 4096 Jul 2 10:49 label drwxrwxr-x 4 zribi.f scalp 4096 Jul 5 17:12 mri drwxrwxr-x 2 zribi.f scalp 4096 Jul 9 10:44 scripts drwxrwxr-x 2 zribi.f scalp 4096 Jul 2 10:49 SD drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 src drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 stats drwxrwxr-x 6 zribi.f scalp 4096 Jul 9 10:44 surf drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 tmp drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 touch drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 trash 2013/7/10 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > I meant can you run it and send us the results? If we can't open the file > it is not an FS issue, but something with the file system. Run ls -l with > the same path that you are giving mris_register > > > Bruce > > > On Wed, 10 Jul 2013, fatma zribi wrote: > > Hi Bruce, >> Yes i can run ls -l in the directory >> >> >> 2013/7/10 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Fatma >> >> are you sure you don't have a typo in the path? Can you run ls -l >> on that file? >> Bruce >> On Wed, 10 Jul 2013, fatma zribi wrote: >> >> >> >> ---------- 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. >> >> >> >> >> >> >>

3 8

polar angle and eccentricity with different parameters
by Bianca van Kemenade 11 Jul '13

11 Jul '13

Dear Freesurfers, When I only had 3 runs of polar angle data for retinotopic mapping, I used for example this command to make the analysis: mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 12 -paradigm rtopy.par -fwhm 5 -fsd bold For some new subjects I have 3 runs of polar angle mapping and 3 runs of eccentricity mapping, with different parameters (cycle duration differs). Is it possible to analyse polar angle and eccentricity in one go? If so, what do I put under the -retinotopy flag? Thanks, Bianca -- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/

2 2

Reconstruction of the rat pial surface
by Shani Ben Amitay 11 Jul '13

11 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 _______________________________________________ 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.

1 0

Questions regarding QDEC
by jh kim 10 Jul '13

10 Jul '13

Dear FreeSurfer experts... Please be patient with a newbie's questions. For the first time, I'm trying to analyze between-group differences in cortical thickness (controls vs. patients) by using FS 5.1.0 and QDEC. I've read through the online manual and mailing lists; however, I cannot figure out the following queries. 1) I selected 'group' (con, pat) as a fixed factor (gender is not applicable because all are females), and demeaned age as a continuous covariate. After analyzing using DODS option, several questions are shown in the Display GUI panel. Does the question "Does the average thickness differ between con and pat?" mean between-group difference of cortical thickness after *controlling for the effect of age*? 2) Should I include average cortical thickness of the left or right cortex (calculated from the command, mris_anatomical_stats -l lh.cortex.label -f subid.txt subid lh) as a nuisance variable? I know this issue has been addressed many times before, and it is generally recommended not to include as a nuisance factor. However, in case of statistically significant difference in mean cortical thickness of one hemisphere (unpaired two sample t-test by SPSS), is it still not necessary to include it as a nuisance factor? From the similar points of view, how about volume and surface area analyses (include or not total cortical volume and total surface area as a nuisance factor, respectively) ? 3) I found several significant clusters that are corrected for multiple comparisons using Monte Carlo simulation (corrected P < 0.01) in the bottom of Display panel. I assume that this procedures take 10,000 permutations by default. Am I right? 4) Last question, how can I extract individual value (cortical thickness per subject) from the significant clusters? I want to do this 'all-at-once'. Please let me know the command. Apology for bothering you. Any comments would be greatly appreciated. Thanks. Kim

3 5

freesurfer registration problem
by Lijia Wang 10 Jul '13

10 Jul '13

Hi experts, When I'm pre-processing the 4D whole brain BOLD images using "preproc-sess -sf -mni305 -fwhm 5 -fsd bold -per-run" , the results of registration from BOLD images to the MNI305 template are always only a small part of the original images. I tried to use another T1_152 template instead(higher resolution) of the original MNI305 template, then"recon-all", "preproc-sess", but the results still remain the small part. How can I solve this problem? Thanks! Best Regards! Rebecca

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