Freesurfer January 2013

freesurfer@nmr.mgh.harvard.edu

111 participants
203 discussions

mean cluster thickness in qdec
by Berg, S.F. van den 14 Jan '13

14 Jan '13

Dear Freesurfer Experts, I would like the mean thickness measures of each cluster i found in qdec. I used qdec for a group comparison in cortical thickness between a patient group and a healthy control group. I found 5 different significant clusters. I would like to extract the mean cortical thickness of each significant cluster in the patient group and in the healthy control group. If this is not possible the mean cortical thickness of the peak/max vertex is also enough information. Where can i found the file with this information? the problem is what do i have to do? run mri_glmfit-sim? but qdec do not create a .glmdir file? so do i have to run the mri_glmfit first? or is mri_glmfit-sim enough but where is the .glmdir file? I use mri_glmfit-sim --glmdir ?.glmdir --sim mc-z 10000 1.3 mc-z.negative --sim-sign abs --cwpvalthresh 0.5 --overwrite I want to create the csdbase.y.ocn.dat (explaind in mri_glmfit-sim --help) for the mean cluster thickness. This is the file where i can find the mean thickness of each cluster, right? A jpeg file is attached to this email. Many thanks, Stan

2 3

Re: [Freesurfer] Freesurfer fails
by Franklin, Crystal G 14 Jan '13

14 Jan '13

Bruce, I have visually checked the transforms and they do indeed seem incorrect. The images are stretched. I have attached the talairach.xfm for one of the images that failed and one that worked. Thanks for all your help, Crystal On 1/13/13 3:08 PM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >can you cc the list? Have you visualized the transform to see if it is >indeed incorrect? > >On Sun, 13 Jan 2013, Franklin, Crystal G wrote: > >> I used mri_convert to create the 001.mgz file. In freeview the >>directions appear correct. >> >> Thanks, >> Crystal >> -----Original Message----- >> From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Date: Sun, 13 Jan 2013 09:02:16 >> To: Franklin, Crystal G<FRANKLINC(a)uthscsa.edu> >> Cc: Freesurfer(a)nmr.mgh.harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] Freesurfer fails >> >> Hi Crystal >> >> how did you create the 001.mgz? When you view it in freeview does >> freeview have the correct directions in the anatomy (i.e. I/S, A/P and >> L/R)? >> >> cheers >> Bruce >> On Sat, 12 Jan 2013, Franklin, Crystal G wrote: >> >>> Freesurfer, >>> >>> I have been running a group of subjects through recon-all and some of >>>the >>> subjects are failing at the very beginning of the process and I am not >>>sure >>> why. The images look fine, but I keep getting the following error: >>> >>> #@# Talairach Failure Detection Fri Dec 7 10:54:57 CST 2012 >>> /Applications/freesurfer/subjects/PHY002/mri >>> \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n >>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >>> ***FAILED*** (p=0.0013, pval=0.0000 < threshold=0.0050) >>> INFO: Attempting MINC mritotal to perform Talairach align >>> >>> Do you know what could be causing this? >>> >>> I read that you can include the command ?notal ?check to skip this >>>test, but how >>> will this effect my data? If I run this command on the subjects that >>> failed and combine their results with the subjects that worked will my >>>group >>> results be effected? >>> >>> Any help would be appreciated. I have attached one of the log files >>>for a >>> subject that failed. >>> >>> Thanks, >>> Crystal >>> >>> >> >> >> 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. >> >> >>

2 1

Registering individual subjects to MNI152
by Shantanu Ghosh 14 Jan '13

14 Jan '13

Dear freesurfer experts, I have .sig maps of cortical thickness, curvature and sulcal depth measures from my dataset (two groups: patient, control). I have the following questions: 1) I want to overlay all three maps simultaneously on an average subject created from all subjects' brains, with different color maps. Which command will do this? 2) Register all ?h.thickness datasets to mni152 instead of mni305/fsaveage, convert the files to .mnc/.obj format, and read in Matlab. In this step, do I have to convert the native ras coordinates too? If I want to use bbregister for this step, can you specify the commandline to do this? 3) I want to compute vertexwise expansion/contraction for local surface area, by a) calculating total surface area of all faces connected to a vertex, and then multiplying it with corresponding curv and sulc of that vertex, and b) comparing the result in 3a) with the warpfield from the registration form step 2) above. Or is there something I am missing here? Also, for 3a) how do I get the correct set of triangles for each vertex? Thanks in advance, Shantanu -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging

2 2

Clarification regarding eTIV
by Salil Soman 13 Jan '13

13 Jan '13

Dear List Members, I am planning to use the eTIV for a group analysis using segmentation volumes and I need to confirm that the eTIV ( aka ICV) generated in freesurfer is NOT dependent on the skull strip? Specifically, I wanted to make sure one does not need to QC the skull strips to make sure all of the brain structures suggested in that figure on p728 of the buckner paper ( http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV?action=AttachFile&do=view&tar…) need to be included? Thanks, -S

1 0

What is the correct way to cite Freesurfer in a journal paper?
by john.drozd＠gmail.com 13 Jan '13

13 Jan '13

Hello, I am writing a paper for publication in Neuroimage. I used Freesurfer 4.3 to segment brain anatomy. Lateral ventricles were my focus. Can someone please tell me what is the correct way to cite Freesurfer in a bibliography? Is there a paper I can cite? Thank you, John Drozd John Jan Drozd, M.Sc., Ph.D. Financial Secretary Knights of Columbus St. Pius X Council 10561 Holy Family Parish Post-Doctoral Scholar (Fellow) Imaging Department Robarts Research Institute Western University London, ON, Canada http://publish.uwo.ca/~jdrozd2 http://kong.apmaths.uwo.ca/~jdrozd/personal.html http://kong.apmaths.uwo.ca/~jdrozd/bio.html http://cfmm.robarts.ca/people/staff/bartha-group/#john cell phone: 519-282-3340

3 2

Freesurfer fails
by Franklin, Crystal G 13 Jan '13

13 Jan '13

Freesurfer, I have been running a group of subjects through recon-all and some of the subjects are failing at the very beginning of the process and I am not sure why. The images look fine, but I keep getting the following error: #@# Talairach Failure Detection Fri Dec 7 10:54:57 CST 2012 /Applications/freesurfer/subjects/PHY002/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0013, pval=0.0000 < threshold=0.0050) INFO: Attempting MINC mritotal to perform Talairach align Do you know what could be causing this? I read that you can include the command –notal –check to skip this test, but how will this effect my data? If I run this command on the subjects that failed and combine their results with the subjects that worked will my group results be effected? Any help would be appreciated. I have attached one of the log files for a subject that failed. Thanks, Crystal

2 1

Analysis ROI between two levels
by xiangbo_2010＠126.com 13 Jan '13

13 Jan '13

发送自我的HTC One SU ----- Forwarded message ----- 发件人： "xiangbo_2010" <xiangbo_2010(a)126.com> 收件人： "MCLAREN, Donald" <mclaren.donald(a)gmail.com> 抄送： <freesurfer(a)nmr.mgh.harvard.edu> 主题： [Freesurfer] contrast matrix 日期：周二, 12 月 11 日, 2012 年 20:08 Dear experts I had obtained a ROI through the interaction between factor 1(A,B) and factor 2(C,D,E), the following: I want to detect the difference between C and D in this ROI. Whether it was done using Freesurfer? thanks! Bo Xiang At 2012-12-02 05:24:18,"MCLAREN, Donald" <mclaren.donald(a)gmail.com> wrote: >Bo Xiang got the following Error Message. Attached are the mtx and >fsgd file. Does anyone what caused the error? > >> >>On Fri, Nov 30, 2012 at 8:28 AM, xiangbo_2010 <xiangbo_2010(a)126.com> wrote: >>> Dear Donald McLaren >>> >>> I used the contrast to run, but the error is appear: >>> >>> mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd COMTthreeinteryes.fsgd >>> dods --C COMTthreeinteryes.mtx --surf fsaverage rh --cortex --glmdir >>> lh.COMTthree.glmdir >>> >>> gdfReadHeader: reading COMTthreeinteryes.fsgd >>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. >>> Continuous Variable Means (all subjects) >>> 0 age 26.2227 11.3891 >>> Class Means of each Continuous Variable >>> 1 MAC 23.9333 >>> 2 MAD 23.5455 >>> 3 MAE 24.5000 >>> 4 MBC 28.6923 >>> 5 MBD 26.3158 >>> 6 MBE 30.3750 >>> 7 FAC 24.1707 >>> 8 FAD 26.4643 >>> 9 FAE 25.0909 >>> 10 FBC 25.9130 >>> 11 FBD 31.5217 >>> 12 FBE 34.0000 >>> INFO: gd2mtx_method is dods >>> Reading source surface /media/freesurfer1/CT/fsaverage/surf/rh.white >>> Number of vertices 163842 >>> Number of faces 327680 >>> Total area 65020.765625 >>> AvgVtxArea 0.396850 >>> AvgVtxDist 0.717994 >>> StdVtxDist 0.193566 >>> >>> $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ >>> cwd /media/freesurfer1/CT >>> cmdline mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd >>> COMTthreeinteryes.fsgd dods --C COMTthreeinteryes.mtx --surf fsaverage rh >>> --cortex --glmdir lh.COMTthree.glmdir >>> sysname Linux >>> hostname psylab-desktop >>> machine x86_64 >>> user psylab >>> FixVertexAreaFlag = 1 >>> UseMaskWithSmoothing 1 >>> OneSampleGroupMean 0 >>> y /media/freesurfer1/CT/lh.gender_age.thickness.10.mgh >>> logyflag 0 >>> usedti 0 >>> FSGD COMTthreeinteryes.fsgd >>> labelmask /media/freesurfer1/CT/fsaverage/label/rh.cortex.label >>> maskinv 0 >>> glmdir lh.COMTthree.glmdir >>> IllCondOK 0 >>> ReScaleX 1 >>> DoFFx 0 >>> Creating output directory lh.COMTthree.glmdir >>> Loading y from /media/freesurfer1/CT/lh.gender_age.thickness.10.mgh >>> INFO: gd2mtx_method is dods >>> Saving design matrix to lh.COMTthree.glmdir/Xg.dat >>> Normalized matrix condition is 82.694 >>> Matrix condition is 73313.7 >>> Found 149926 points in label. >>> Pruning voxels by thr: 0.000000 >>> Found 149926 voxels in mask >>> Saving mask to lh.COMTthree.glmdir/mask.mgh >>> Reshaping mriglm->mask... >>> search space = 74490.928733 >>> MatrixReadTxT: could not scan value [3][1] >>> >>> ERROR: loading C COMTthreeinteryes.mtx >>> >>> thanks! >>> >>> Bo Xiang >>> >>> >>> >>> >>> >>> At 2012-11-30 06:25:12,"MCLAREN, Donald" <mclaren.donald(a)gmail.com> wrote: >>>>Yes. >>>> >>>>Best Regards, Donald McLaren >>>>================= >>>>D.G. McLaren, Ph.D. >>>>Research Fellow, Department of Neurology, Massachusetts General Hospital >>>> and >>>>Harvard Medical School >>>>Postdoctoral Research Fellow, GRECC, Bedford VA >>>>Website: http://www.martinos.org/~mclaren >>>>Office: (773) 406-2464 >>>>===================== >>>>This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED >>>>HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is >>>>intended only for the use of the individual or entity named above. If the >>>>reader of the e-mail is not the intended recipient or the employee or agent >>>>responsible for delivering it to the intended recipient, you are hereby >>>>notified that you are in possession of confidential and privileged >>>>information. Any unauthorized use, disclosure, copying or the taking of any >>>>action in reliance on the contents of this information is strictly >>>>prohibited and may be unlawful. If you have received this e-mail >>>>unintentionally, please immediately notify the sender via telephone at >>>> (773) >>>>406-2464 or email. >>>> >>>> >>>>On Wed, Nov 28, 2012 at 3:27 AM, xiangbo_2010 <xiangbo_2010(a)126.com> wrote: >>>>> Dear Donald McLaren >>>>> >>>>>>> I want to make interaction between factor 1 (A,B) and factor 2 >>>>>>> (C,D,E). >>>>>>> age >>>>> >>>>>>> and gender (M,F) >>>>>>> as covariates, I can get 12 classes: ACM ADM AEM BCM BDM BEM ACF ADF >>>>>>> AEF >>>>>>> BCF BDF BEF and make the contrast: >>>>>>> >>>>>>> +ACM -ADM 0 -BCM +BDM 0 +ACF -ADF 0 -BCF +BDF 0 age age age age age age >>>>>>> age age age age age age >>>>>>> 0 +ADM -AEM 0 -BDM +BEM 0 +ADF -AEF 0 -BDF +BEF age age age age age age >>>>>>> age age age age age age >>>>> because the age an

1 0

error: could not read 65536 bytes at slice 76 in skull stripping process
by Sandra Preissler 12 Jan '13

12 Jan '13

Dear freesurfer users, I have an unexpected error using autorecon1. The error occurred during the skull stripping process of a person called PTpost_P04. First I tried: recon-all autorecon1 s PTpost_P04 After the first error (recon-all -s PTpost_P04 exited with ERRORS) I checked the logfile and tried the following: cd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri followed directly by: mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz I became the error message: could not read 65536 bytes at slice 76 The information about the freesurfer version and linux version used are: FREESURFER_HOME: /opt/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Kernel info: Linux 2.6.34.10-0.6-default x86_64 It would be great if anybody could help me in solving this. Best regards Sandra ---------------------------------------------------------------- This message was sent through https://webmail.uni-jena.de

3 4

Re: [Freesurfer] QA Tools Snaps Scrambled - Follow up
by Irwin, William 12 Jan '13

12 Jan '13

Hi Louis- I dug a little deeper and examined the rgb files before conversion. The problem is not with the IM conversion, it is with the capture. For example, '<subject>_curv_lh_lat.rgb' is just fine, but from the same subject 'snapshot-talairach-H-128.rgb' is garbage. Any ideas on this? Thanks, Wil -----Original Message----- From: Irwin, William Sent: Wednesday, January 09, 2013 6:22 AM To: Louis Nicholas Vinke Cc: freesurfer(a)nmr.mgh.harvard.edu; Irwin, William Subject: RE: [Freesurfer] QA Tools Snaps Scrambled - Clairification Hi Louis- I was speaking cryptically and/or imprecisely. Of course there are dependencies for IM-- in fact about 8 libraries which are uniquely required by IM. I was thinking about a higher (or lower) level of dependency. This would suggest a more system-level problem, but I'm not having problems with any of the other apps running on my system. Obviously I'm not asking you to help diagnose the health of my system, but though you might have some thoughts/suggestions. Regards, Wil -----Original Message----- From: Irwin, William Sent: Wednesday, January 09, 2013 5:37 AM To: Louis Nicholas Vinke Cc: freesurfer(a)nmr.mgh.harvard.edu; Irwin, William Subject: RE: [Freesurfer] QA Tools Snaps Scrambled Hi Louis- No problem doing command line conversion of an rgb to either jpg or gif in terms of error messages. However, the converted files are scrambled. Might there be a dependency on which ImageMagick relies which still in place, but corrupted? I was under the impression ImageMagick was self-contained. This is a real mystery -Wil -----Original Message----- From: Louis Nicholas Vinke [mailto:vinke@nmr.mgh.harvard.edu] Sent: Tuesday, January 08, 2013 6:29 PM To: Irwin, William Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QA Tools Snaps Scrambled Hi Irwin, It sounds like the snapshots from tksurfer are fine, but the ones from tkmedit are not being generated properly. It may be this peculiar bug where ImageMagick has trouble reading rgb files. Try converting an rgb file to a jpg 'convert file.rgb file.jpg'. You may get the error 'Improper image header'. The tksurfer tcl script saves tiff files, the tkmedit tcl script saves rgbs, which may explain why some images are fine. -Louis On Tue, 8 Jan 2013, Irwin, William wrote: > > Hi- > > > > I’ve come across a peculiar behavior with recon_checker, and am hoping > someone can shed some light on this. > > > > I have used it 100’s of times in the past, but not for about 2 months. > I recently processed a large set of cases I wanted to QC. When I ran > it, some, but not all, of the snaps were corrupted. Specifically the > talairach, aseg, surfs, and all the ‘detailed snaps’, which are > basically additional instances of the aforementioned types. The > inflated, curv, and parc are all just fine. As the process runs, all > images are being displayed in the pop-up windows, and the html page is created. > > > > While there have been no system changes which should affect this, I > upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the > problem. The problem remains. And the problem remains w/ or w/o the > flag for detailed snaps. > > > > If all of the images were corrupted, I would have certainly concluded > something has gone awry with my system. The fact that only some of the > images are corrupted makes me scratch my head. > > > > Thoughts? Suggestions? > > > > Thanks, > > Wil > > > 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.

2 1

recon-all process on brain regions of interest
by ZhiLiangLong 12 Jan '13

12 Jan '13

Hi everyone: I met problem about the recon-all process. I got some brain regions showing group-differences of activation in task. Now, i want to compare the difference of cortical thickness on these brain regions. I prefer to limit the compution of cortical thickness on my regions of interest rather than the whole brain to reduce compution time. But i do not know how the recon-all works it out. I need your suggestions. In addition, assume that i have finished recon-all process on the whole brain, how can i obtain the cortical thickness of my regions of interest? All the best!

2 1

← Newer
1
...
12
13
14
15
16
17
18
...
21
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 January 2013