[Freesurfer] how to generate statistics after segmentation of hippocampal subfields
Hi experts, After segmentation of hippocampal subfields, how to generate statistics of the subfield regions, such as volume? Thank you Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0...@gmail.com / wangkangcheng@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] meaning of foldind
Dear experts, In the Group stats files, there is a file of lh.a2009s.foldind (or rh.a2009s.foldind). What's the meaning of foldind? Thank you Wang Kangcheng ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Problem of VolumeRoiCorticalThickness
Dear Bruce, Now, I change the standard atlas to avg152T1.nii.gz which was included in the FSL and make a mask of superior frontal gyrus (Harvard-Oxford Cortical Structural Atlas). I can map the ROI-mask to the fsaverage surface to create an fsaverage-ROI surface overlay. But when I map one subject thickness data to the fsaverage subject using the following command: mri_surf2surf --s s12129 --trgsubject fsaverage --hemi lh --sval s12129/surf/rh.thickness --tval ~/Desktop/mask/rh.thickness.fsaverage.mgh --reshape it said: Reading source surface reg /Users/wangkangcheng/Desktop/dataplus_60/s12129/surf/lh.sphere.reg Loading source data ERROR: dimension inconsistency in source data Number of surface vertices = 146027 Number of value vertices = 145656 How could solve this problem? Thank you Wang Kangcheng ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Problem of VolumeRoiCorticalThickness
Dear Bruce, I try to extract freesurfer cortical thickness valunes for a ROI defined in volume space (avg152T1.nii.gz). I try a lot and have extracted the values successfully now. Thank you very much. I suggest the experts can change opition --reshape of mri_vol2surf and mri_surf2surf into --noreshape. If I use opition of reshapre, it always report the errors of dimension. Thank you Wang Kangcheng From: Bruce Fischl Date: 2014-06-16 21:04 To: kangchengwang0...@gmail.com CC: freesurfer Subject: Re: [Freesurfer] Problem of VolumeRoiCorticalThickness Hi Wang you can't change the atlas that way. We extract a ton of information and store it in what we call an atlas, and what we require isn't in the harvard-oxford one. What are you trying to achieve? cheers Bruce On Mon, 16 Jun 2014, kangchengwang0...@gmail.com wrote: Dear Bruce, Now, I change the standard atlas to avg152T1.nii.gz which was included in the FSL and make a mask of superior frontal gyrus (Harvard-Oxford Cortical Structural Atlas). I can map the ROI-mask to the fsaverage surface to create an fsaverage-ROI surface overlay. But when I map one subject thickness data to the fsaverage subject using the following command: mri_surf2surf --s s12129 --trgsubject fsaverage --hemi lh --sval s12129/sur f/rh.thickness --tval ~/Desktop/mask/rh.thickness.fsaverage.mgh --reshape it said: Reading source surface reg /Users/wangkangcheng/Desktop/dataplus_60/s12129 /surf/lh.sphere.reg Loading source data ERROR: dimension inconsistency in source data Number of surface vertices = 146027 Number of value vertices = 145656 How could solve this problem? Thank you Wang Kangcheng 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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Problem of VolumeRoiCorticalThickness
Dear Douglas Greve, Thank you very much. I change it and change the option of reshape into noreshape. Then, it could be sucessful. ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] How to extract significant result for each subject
Dear freesurfers, I contrast depression and control and find that patients have a lower thickness in region of inferior frontal gyrus. Now, I want to extract the data of thickness for each subject. Could you tell which command could do this? Thank you Wang Kangcheng ( New learner of freesurfer ) ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] 回复: Re: LGI error
Hi Marie Schaer, Thank you very much. I hope other experts could help me.
Kangcheng
Wang Kangcheng
Faculty of Psychology, Southwest University, China
Email: kangchengwang0...@gmail.com / wangkangcheng@163.com
Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China
发件人： Marie Schaer
发送时间： 2013-12-07 02:46
收件人： 王康程
抄送： freesurfer@nmr.mgh.harvard.edu
主题： Re: [Freesurfer] LGI error
Hi Kangchen,
I also had the same error recently on a unix machine, but I unfortunately did
not find the solution and some help would be greatly appreciated.
I think that the bug is due to the fact that make_outer_surface.m calls
MRIread.m, which calls load_mgh.m and that something gets wrong at the point of
reading the file (and removing temporary files). But I'm afraid I can't help
more, I tried to edit load_mgh to add -f after rm and it didn't help.
Nick or Doug, any idea?
Many thanks in advance!
Marie
On Dec 6, 2013, at 5:31 AM, 王康程 kangchengwang0...@gmail.com wrote:
Dear all，
When I run recon-all -s ${subject} -localGI, it appear rm: remove regular
file `/tmp/tmp4653077.mgh'? . Then, I write yes, however, it didn't response
anyway. How shold I do next? Thank you!
The echo for the process is followed
--
running subject Emotion_xunlian_s12002
--
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /home/fmri/desktop/test
Actual FREESURFER_HOME /usr/local/freesurfer
-rw-rw-r--. 1 root root 544815 Dec 6 20:54
/home/fmri/desktop/test/Emotion_xunlian_s12002/scripts/recon-all.log
Linux localhost.localdomain 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16
18:37:12 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
/home/fmri/desktop/test/Emotion_xunlian_s12002/surf
#
#@# Local Gyrification Index lh Fri Dec 6 21:07:40 CST 2013
mris_compute_lgi --i lh.pial
=
rm -Rf
/home/fmri/desktop/test/Emotion_xunlian_s12002/surf/tmp-mris_compute_lgi-lh.pial
=
=
mkdir -p
/home/fmri/desktop/test/Emotion_xunlian_s12002/surf/tmp-mris_compute_lgi-lh.pial
=
=
mris_fill -c -r 1 lh.pial
/home/fmri/desktop/test/Emotion_xunlian_s12002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=
reading surface from lh.pial...
writing filled volume to
/home/fmri/desktop/test/Emotion_xunlian_s12002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
conforming output volume
setting resolution for intermediate calculations to 1.
=
make_outer_surface('/home/fmri/desktop/test/Emotion_xunlian_s12002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/home/fmri/desktop/test/Emotion_xunlian_s12002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
exit
=
Warning: Unable to open display 'iconic'. You will not be able to display
graphics on the screen.
M A T L A B (R)
Copyright 1984-2012 The MathWorks, Inc.
R2012a (7.14.0.739) 64-bit (glnxa64)
February 9, 2012
Toolbox Path Cache read in 0.02 seconds.
MATLAB Path initialized in 0.79 seconds.
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
reading filled volume...
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /home/fmri/desktop/test
MNI_DIR /usr/local/freesurfer/mni
FSL_DIR /opt/fsl
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /home/fmri/desktop/test
MNI_DIR /usr/local/freesurfer/mni
FSL_DIR /opt/fsl
rm: remove regular file `/tmp/tmp4653077.mgh'?
--
kangcheng Wang
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