Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

How to design the contrast matrix with 12 regressors?
by 李仕广 26 Nov '12

26 Nov '12

Dear FreeSurfers: I hope you can help me out with a problem in disgning my .mtx file. I want to examine the difference among three groups (HC group, EX group and PT group). Considing gender, I have six groups as similar as the example described inhttp://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf6G0V. But I want to correct for age. Then, I have 6 classes (two factors/three levels) and one covariate (age). How can I compare the difference among three groups (HC group, EX group, and PT group)? Could you please tall me how to design the contrast matrix with 12 regressors? Thanks a zillion times! Best wishes shiguangli

3 3

registration Fail
by Gabriel Gonzalez Escamilla 26 Nov '12

26 Nov '12

2 1

Re: [Freesurfer] fieldsign-sess problem in retinotopy
by Zhou, Wei 26 Nov '12

26 Nov '12

Hi Doug, Thank you for reply. As in rtopy.par the stimtype is either polar or eccen, I get separate f.nii files for eccen and polar and do one of the two at one time. Do you mean I should combine polar and eccen sessions into one f.nii? e.g. i want to do polar analysis whose rtopy.par file is polar, but I still need to put eccen session into f.nii with polar and then do the analysis? Best Wei ----------- Hi Wei, do you have both polar and eccentricity? It looks like you only have polar. doug On 11/19/2012 01:39 PM, Zhou, Wei wrote: > Please find the Xtmp.mat in the attachment.Thank you, Doug. > Best > Wei > ---- > Can you send me the Xtmp.mat file? > dloug > > On 11/16/2012 01:01 PM, Zhou, Wei wrote: > > Hi Doug, > > > > It seems the previous fieldsign-sess problem is due to that I stored > > data on one server while freesurfer is on the other server. > > But when I put the data and freesurfer on the same server and run the > > retinotopy analysis again, it reported fail msg for "selxavg3-ses" : > > -- > > ntptot = 80, nX = 27, DOF = 53 > > Saving X matrix to > > > > /media/local_home/zhouw4/testf/retinotopy/SUBJ01/bold/rtopy.self.lh/Xtmp.mat > > Error using svd > > Input to SVD must not contain NaN or Inf. > > > > Error in cond (line 39) > > s = svd(A); > > > > Error in fast_selxavg3 (line 254) > > XCond = cond(XtX); > > --- > > I checked Xtmp.mat. There is NaN in Xn and XtX. > > My rtopy par is: eccen and pos. > > > > Would you please give me some idea about this error? > > > > Best > > Wei > > > > >> > > Try using this version > > > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fieldsign-sess > > > > doug > > > > On 11/01/2012 11:47 AM, Zhou, Wei wrote: > > > Hi Doug, > > > > > > The subject name for structural is "SUBJ1" when I did recon-all, which > > > is also the content of file "subjectname". My dir structures of > > > "structural" and "retinotopy" are the same as > > > http://www.alivelearn.net/?p=65 . "SUBJ1" is stored under > > > "structural". if I set SUBJECTS_DIR as "....../structural", > > > $SUBJECT_DIR/SUBJ1 does exist, then still I get the same error msg. > > > > > > The following is the log file: > > > > > > fieldsign-sess log file $Id: fieldsign-sess,v 1.2 2010/05/04 22:00:18 > > > greve Exp $ Thu Nov 1 10:36:52 CDT 2012 Linux rii-appserv-02 > > > 2.6.32-279.11.1.el6.x86_64 #1 SMP Sat Sep 22 07:10:26 EDT 2012 x86_64 > > > x86_64 x86_64 GNU/Linux /media/users/zhouw4/testf/retinotopy > > > /usr/local/freesurfer/fsfast/bin/fieldsign-sess -a rtopy.self.lh > > > -occip -s SUBJ1 uid=20120(zhouw4) gid=22000(rii_users) > > > groups=22000(rii_users),21100(rii_appservers),23000(domain^users) > > > context=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023 > > > > > > Best > > > Wei > > > > > > > > > >What is the name of FreeSurfer subject? This is not necessarily the > > > same>> > > > >as SUBJ01 in your command line below. That is the session (which may > > or > > > >may not be the same as the "subject name"). What ever the subjectname > > > is, does SUBJECT_DIR/subject exist? > > > On 10/31/2012 03:07 PM, Zhou, Wei wrote: > > > > > > > > Hi, Doug > > > > > > > > Thank you for your reply. I have tried exporting SUBJECTS_DIR to > > the > > > > directory of upper fold, retinotopy or SUBJ01 But none of them > > works. > > > > Still the same error msg. > > > > > > > > So what should SUBJECTS_DIR be exported to for this analysis? > > > > > > > > Best > > > > > > > > Wei > > > > > > > > > > > > > > > > >Hi Wei, this is a bug in the error msg. It is trying to say that > > your > > > > >source subject is not in the $SUBJECTS_DIR. > > > > >doug > > > > > > > > >On 10/27/2012 02:27 PM, Zhou, Wei wrote: > > > > > Dear freesurfers, > > > > > > > > > > I am trying retinotopy analysis in freesurfer. For > > > "fieldsign-sess", I > > > > > encounter the following problem when I type "fieldsign-sess > > -a > > > > > rtopy.self.lh -occip -s SUBJ01" or "fieldsign-sess -a > > > rtopy.self.lh > > > > > -occip -sf sessid": > > > > > > > > > > > > > */media/users/zhouw4/testf/retinotopy/SUBJ01/log/fieldsign-sess.log* > > > > > *subject: Undefined variable.* > > > > > > > > > > my structure of retinotopy fold is : > > > > > retinotopy > > > > > | |--sessid > > > > > |--SUBJ01 > > > > > |--subjectname > > > > > > > > > > |--bold > > > > > |--001 > > > > > |--f.nii > > > > > |--rtopy.par| > > > > > > > > > > I really appreciate it if you could give me some idea about > > that > > > > > problem. Thanks a lot in advance. > > > > > > > > > > Best > > > > > Wei Zhou > > > > > Medical Physics Ph.D. Student > > > > > Diagnostic Imaging Track > > > > > cgxz...(a)gmail.com<mailto:cgxz...@gmail.com> > > > > > > > zho...(a)livemail.uthscsa.edu<mailto:zho...@livemail.uthscsa.edu> > > > > > > > > > > > > > > > _______________________________________________ > > > > > 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 > > > > gr...(a)nmr.mgh.harvard.edu > > > > Phone Number: 617-724-2358 > > > > Fax: 617-726-7422 > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > Best > > > Wei Zhou > > > Medical Physics Ph.D. Student > > > cgxz...(a)gmail.com<mailto:cgxz...@gmail.com> > > > zho...(a)livemail.uthscsa.edu<mailto:zho...@livemail.uthscsa.edu> > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > Best > > Wei Zhou > > > > > > > > _______________________________________________ > > 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 > gr...(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Best > Wei Zhou > > > > _______________________________________________ > 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 gr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

2 1

spline_smooth crash (NEW problem)
by Negar Memarian 26 Nov '12

26 Nov '12

Dear FreesSurfers, **I've checked similar posts on the email-list and still could not find an answer to my question. I'd really appreciate your attention and feedback: recon-all -autorecon1 crashes for me in one of the steps before skull stripping with an error like this: Done spline_smooth: posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed. nu_estimate_np_and_em: crashed while running spline_smooth (termination status=6) nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC2009 i686GNU/Linux recon-all -s BT501_FS exited with ERRORS at Mon Nov 26 15:26:10 EST 2012 I made sure that I have the newest version of FreeSurfer, the environment variables MNI_DATAPATH and MNI_PERL5LIB and PERL5LIB exist and I ran $FREESURFER_HOME/bin/fixup_mni_paths as well. But unfortunately I still face the same problem. I also tried the process for a different subject, but the same error. Does anyone have any idea how I can fix this? I have attached the recon-all.log file. I'd really appreciate your help. Negar Negar Memarian, MASc, PhD NSERC Postdoctoral Fellow Department of Neurology David Geffen School of Medicine at UCLA

1 0

p-value too small?
by Caspar M. Schwiedrzik 26 Nov '12

26 Nov '12

Hi! I ran into a funny problem when calculating contrasts in Freesurfer 4.5.0. Namely, the center of my cluster of significant voxels has a p-value of -0.0, resulting in a funny whole where you would otherwise expect to find the most significant voxel(s). It seems that the p-value is too small. Is there a workaround available? Thank you very much, Caspar

2 1

Re: [Freesurfer] Subgroup analysis
by Mahinda Yogarajah 26 Nov '12

26 Nov '12

Hi Doug and Donald, Again many thanks for the advice. With regard to the analysis described previously - I have n=21 in my control group while P1=4 patients, P2=7 patients, P3=3 patients and P4=5 patients. Given that i have small numbers I elected to compare only 2 patient groups (p1 and p4) rather than all 4. My aim was to show that P4 patients (higher level of endogenous factor) are more affected (eg smaller area and greater thickness-age decline compared to controls) than P1. Given that as Donald points out that (c-p1) - (c-p4) is like comparing p1 and p4 directly, I did the latter but there is nothing significant. However when i compare p1 to controls and then p4 to controls separately i see nothing signficant in the p1 analysis but significant results in the p4 analysis - this makes sense as the p4 gp are more affected than the very mild p1 gp. My questions are: 1) why the difference in results between the two analyses (? due to larger overall group in second analysis) 2) is the latter analysis valid ? Thanks for your help. Mahinda

2 1

topological defect correction: Orig surface is right but WM surface is not right
by 嘉逸劉 26 Nov '12

26 Nov '12

Hello FS experts, I have a MRI volume where there is regional hyperintensity at cortex and thus the segmentation takes that regional cortex as white matter. In other words, the segmentation process is too aggressive toward the pial surface. I modifed the WM by manual erase across several slices and run -autorecon2-wm and -autorecon3. However, when I checked the results, I found the "original surface" is right (green color in the appended file; the tesselation is compatible with my manural editing) but the "white matter surface" is not updated (yellor color in the appended file; the surface is not adjusted, just like the old one before my editing). Could anybody guide me how to solve this issue? Thank you very much, JoJo

2 1

rotation applied by mri_convert
by Marie Schaer 26 Nov '12

26 Nov '12

Hi everyone, I have a question related to mri_convert (I use FreeSurfer version 5.1). I noticed that when I convert some images without specifying anything about the orientation (mri_convert MY_DICOMS 001.mgz), in a high proportion of the case, mri_convert will identify an orientation matrix which is not simply made of 0 and 1, like e.g. i_ras = (-0.00872651, -0.999962, 0) j_ras = (-0, -0, -1) k_ras = (-0.999962, 0.00872654, 0) The non integer values result in the application of a slight rotation when converting the images, associated with interpolation and a slight loss in image quality. The only way that I found to avoid that the image quality loss was to run a first time mri_convert to look at these parameters, and then transform them to the nearest integer to feed them to mri_convert. In the example above I would run: mri_convert MY_DICOMS 001.mgz -iid 0 -1 0 -ijd 0 0 -1 -ikd -1 0 0 Given that I don't change the orientation (i.e no flip), but just want to avoid the rotation, I was wondering if there was any better option in mri_convert than what I am currently doing. Many thanks in advance for your answer, Marie

3 2

Info FreeSurfer
by Andrea Tateo 26 Nov '12

26 Nov '12

Hello, I am working on segmentation of the hippocampus and I need a comparing method. I am approaching for the first time to FreeSurfer method. I would like your courteous help. I have three questions for you: 1 - I have input a MRI-image.nii showing all head. As output I would like a binary image showing only left and right hippocampus. I used the following command: ### mri_convert FILE_NAME.nii path/directory/NAME_OUTPUT.mgz recon-all -s SUBJECT_name -autorecon-all ### How can I extract the required binary image? 2 - Is it possible to comput only hippocampus region (to reduce the processing time)? 3 - Is it possible to give as input only an ristrected region of the subject's head? Best regards Andre Tateo

2 1

re reconstructions
by Catherine Bois 26 Nov '12

26 Nov '12

Hi, I am currently in the process of reconstructing my brains after performing edits. I am submitting them to a system named condor, which allows them to be processed in parallel, reducing time. However, I am unsure of how to best use the script that takes into account all the changes made. Is it possible to submit the same script for all (even though different changes have been made to each brain), as long as the command specifying the change occurs earlier in the process than for example the changes made to a certain brain (hope that makes sense). Is this correct? However, I have also heard from someone tha tif you make white matter edits you should only run the reconstruction process at the steps AFTER the white matter mask is created; is this correct? As this is contradictory to what I thought; I thought that you start with your edits that are "earlist in the process"; ie do that step again and then it takes into account subsequent edits? Thanks for your help, sorry for the confusing question. Cathy

2 3

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