Freesurfer July 2013

freesurfer@nmr.mgh.harvard.edu

165 participants
332 discussions

Re: [Freesurfer] (no subject)
by Douglas N Greve 11 Jul '13

11 Jul '13

Hi Nick, please remember to post to the list and not to us personally. To answer your question, you could create an run an analysis with just the button press. Go into the analysis and get the button press regressor from X.mat, then save it as a text file in the run folder. Then make your analysis and specify this as a task regressor. I *think* that should work. doug On 07/11/2013 02:57 PM, Nicholas Paul Denisuk wrote: > Thanks Doug, > > This is actually a retinotopy analysis and the paradigm files are > phase encoded. Is there any possible way to regress out the activity > associated with the button presses. > > Thanks for your assistance, > > Nick > > On 7/9/13, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: >> Why not include it as a condition in your paradigm file? >> doug >> >> >> On 07/09/2013 03:47 PM, Nicholas Paul Denisuk wrote: >>> 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 >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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. >> >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

Re: [Freesurfer] Freesurfer Digest, Vol 112, Issue 41
by Maria Kharitonova 11 Jul '13

11 Jul '13

Hi, sorry I must have missed the response to this a few weeks back. Yes, I'm doing an identical analysis: comparing 2 groups of kids (controls and ADHD) in cortical thickness, controlling for age and demeaned ICV (nuisance). So all the parameters are the same. I'm attaching 3 screen shots: group differences using 5.0 before using Monte Carlo correction (lots of clusters), group differences before correction using 5.3 (few small clusters), and group differences using 5.0 after correction (frontal cluster). there was nothing sig. remaining after correcting for multi. comparisons using 5.3. I'm puzzled about why the differences are so large. I selected DODS in 5.0, so everything should be the same? I triple-checked to make sure the other differences (e.g. FWHM, etc.) were identical (left at default). Thanks! Maria ****** Message: 10 Date: Tue, 18 Jun 2013 23:34:10 -0700 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] qdec differences in FS 5.0 vs 5.3 To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <51C150E2.1080604(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Maria, can you elaborate on exactly what you have done? Is the data the same and you are only changing the version of QDEC? What is the nature of the difference? Can you send pics or stats? doug On 6/18/13 6:06 AM, Maria Kharitonova wrote: > Hi, > > I'm learning how to use QDEC and was comparing results that it produces under FresSurfer 5.0 vs 5.3. I know the 5.0 has an option for either DODS or DOSS method of producing a design matrix, while the 5.3 only has DODS. This suggests that results should be identical (or at least similar) across versions if I select DODS. However, I'm getting very different results based on the version I select: complete lack of differences across groups in 5.3 and a predicted pattern of differences in 5.0 using DODS. I'd like to understand where the differences are stemming from -- any ideas? > > Thanks in advance! > Maria > > ******************************* > > Maria Kharitonova, Ph.D. > Postdoctoral Research Fellow > Laboratories of Cognitive Neuroscience > Boston Children's Hospital > > >

2 6

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. >> >> >> >>

1 0

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

← Newer
1
...
19
20
21
22
23
24
25
...
34
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer July 2013