Dear Ruopeng, Thanks for your help, Ruopeng.I learned the groupanalysis by manu ofhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis. I ran this command on your tutorial data (buckner data). Would you please tell me where my hardware setup is inappropriate? Thanks. All the best.
2014-01-01
charujing
Dear doug, bruce and others, Previously I could not view " freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot " from the "http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis". The freeview did represent 3 images. But it reported a something about no geomatric information and I couldnot configure the overlay(When I clicked the "configure overlay", it stopped without any response). My OS is CentOS 6.5 desktop version, and graphic card is NVIDIA GEFORCE GTX 650 and setup the NVIDIA driver. Freesurfer version is freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz.My computer has 2G memory and 4 processors. I need help to fix it. If anyone have viewed sample data or other data(*.inflated, *sig.cluster.mgh,and *sig.ocn.annot) simultaneously successfully by freeview just as above, would you please tell me some information? The information I need is Freesurer version, Centos version(desktop or others) and something in CentOS setup, graphic card version and its driver, memory size. Thanks very much, doug, brucen and others. Any reply will be highly appreciated. All the best. Rujing Zha
Hi Rujing,
I am able to replicate the issue with 5.3.0 release. The good news is the issue does not appear in the current dev version (so I think it has been fixed). Zeke, would it be possible for Rujing to download a copy of the latest freeview build?
Best, Ruopeng
On Jan 4, 2014, at 10:40 AM, "charujing" charujing@gmail.com wrote:
Dear doug, bruce and others, Previously I could not view " freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot " from the "http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis". The freeview did represent 3 images. But it reported a something about no geomatric information and I couldnot configure the overlay(When I clicked the "configure overlay", it stopped without any response). My OS is CentOS 6.5 desktop version, and graphic card is NVIDIA GEFORCE GTX 650 and setup the NVIDIA driver. Freesurfer version is freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz.My computer has 2G memory and 4 processors. I need help to fix it. If anyone have viewed sample data or other data(*.inflated, *sig.cluster.mgh,and *sig.ocn.annot) simultaneously successfully by freeview just as above, would you please tell me some information? The information I need is Freesurer version, Centos version(desktop or others) and something in CentOS setup, graphic card version and its driver, memory size. Thanks very much, doug, brucen and others. Any reply will be highly appreciated. All the best. Rujing Zha _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Rujing,
Can you please provide me with the contents of the build-stamp.txt file in your $FREESURFER_HOME directory so I can provide you with the correct most up to date version of freeview? Thx.
-Zeke
On Jan 4, 2014, at 2:28 PM, Ruopeng Wang rpwang@nmr.mgh.harvard.edu wrote:
Hi Rujing,
I am able to replicate the issue with 5.3.0 release. The good news is the issue does not appear in the current dev version (so I think it has been fixed). Zeke, would it be possible for Rujing to download a copy of the latest freeview build?
Best, Ruopeng
On Jan 4, 2014, at 10:40 AM, "charujing" charujing@gmail.com wrote:
Dear doug, bruce and others, Previously I could not view " freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot " from the "http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis". The freeview did represent 3 images. But it reported a something about no geomatric information and I couldnot configure the overlay(When I clicked the "configure overlay", it stopped without any response). My OS is CentOS 6.5 desktop version, and graphic card is NVIDIA GEFORCE GTX 650 and setup the NVIDIA driver. Freesurfer version is freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz.My computer has 2G memory and 4 processors. I need help to fix it. If anyone have viewed sample data or other data(*.inflated, *sig.cluster.mgh,and *sig.ocn.annot) simultaneously successfully by freeview just as above, would you please tell me some information? The information I need is Freesurer version, Centos version(desktop or others) and something in CentOS setup, graphic card version and its driver, memory size. Thanks very much, doug, brucen and others. Any reply will be highly appreciated. All the best. Rujing Zha _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Rujing,
You can download the most up to date version of freeview using the following link:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/dev/
In order to use this version, you will need to replace the file $FREESURFER_HOME/bin/freeview.bin currently on your system, with the file you download from the link above. Let me know if you need additional assistance.
-Zeke
Hi Rujing,
I am able to replicate the issue with 5.3.0 release. The good news is the issue does not appear in the current dev version (so I think it has been fixed). Zeke, would it be possible for Rujing to download a copy of the latest freeview build?
Best, Ruopeng
On Jan 4, 2014, at 10:40 AM, "charujing" charujing@gmail.com wrote:
Dear doug, bruce and others, Previously I could not view " freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot " from the "http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis". The freeview did represent 3 images. But it reported a something about no geomatric information and I couldnot configure the overlay(When I clicked the "configure overlay", it stopped without any response). My OS is CentOS 6.5 desktop version, and graphic card is NVIDIA GEFORCE GTX 650 and setup the NVIDIA driver. Freesurfer version is freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz.My computer has 2G memory and 4 processors. I need help to fix it. If anyone have viewed sample data or other data(*.inflated, *sig.cluster.mgh,and *sig.ocn.annot) simultaneously successfully by freeview just as above, would you please tell me some information? The information I need is Freesurer version, Centos version(desktop or others) and something in CentOS setup, graphic card version and its driver, memory size. Thanks very much, doug, brucen and others. Any reply will be highly appreciated. All the best. Rujing Zha _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Ruopeng and Zeke, Thanks. I will try the latest version. CentOS has 6.0,6.1,6.2,6.3,6.4 and 6.5, also part of them have desktop, server and alternate version. And in Freesurfer download page we can see: OSPlatformVersionRelease DateDownloadSize LinuxCentOS 6 x86_64 (64b)stable v5.3.015 May 2013freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz4.2G LinuxCentOS 4 x86_64 (64b)stable v5.3.015 May 2013freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0.tar.gz4.0G LinuxCentOS 4 (32b)stable v5.3.015 May 2013freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz3.8G MacLion OX X 10.7 (64b Intel)stable v5.3.015 May 2013freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg3.5G MacSnowLeopard OS X 10.6 (32b Intel)stable v5.3.015 May 2013freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg3.2G VirtualboxXubuntu 12.04stable v5.3.015 Aug 2013freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz9.0G
Also I want to know which CentOS version(6.0,6.1,6.2,6.3,6.4 or 6.5?) and its desktop, alternate or server I should installed or all of them are appropriate for freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz. Thanks Ruopeng and Zeke. All the best. Rujing Zha
2014-01-05
charujing
发件人：zkaufman@nmr.mgh.harvard.edu 发送时间：2014-01-05 07:10 主题：Re: [Freesurfer] problems about freeview 收件人："charujing"charujing@gmail.com 抄送："Ruopeng Wang"rpwang@nmr.mgh.harvard.edu,"freesurfer"freesurfer@nmr.mgh.harvard.edu,"Z K"zkaufman@nmr.mgh.harvard.edu
Hello Rujing,
You can download the most up to date version of freeview using the following link:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/dev/
In order to use this version, you will need to replace the file $FREESURFER_HOME/bin/freeview.bin currently on your system, with the file you download from the link above. Let me know if you need additional assistance.
-Zeke
Hi Rujing,
I am able to replicate the issue with 5.3.0 release. The good news is the issue does not appear in the current dev version (so I think it has been fixed). Zeke, would it be possible for Rujing to download a copy of the latest freeview build?
Best, Ruopeng
On Jan 4, 2014, at 10:40 AM, "charujing" charujing@gmail.com wrote:
Dear doug, bruce and others, Previously I could not view " freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot " from the "http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis". The freeview did represent 3 images. But it reported a something about no geomatric information and I couldnot configure the overlay(When I clicked the "configure overlay", it stopped without any response). My OS is CentOS 6.5 desktop version, and graphic card is NVIDIA GEFORCE GTX 650 and setup the NVIDIA driver. Freesurfer version is freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz.My computer has 2G memory and 4 processors. I need help to fix it. If anyone have viewed sample data or other data(*.inflated, *sig.cluster.mgh,and *sig.ocn.annot) simultaneously successfully by freeview just as above, would you please tell me some information? The information I need is Freesurer version, Centos version(desktop or others) and something in CentOS setup, graphic card version and its driver, memory size. Thanks very much, doug, brucen and others. Any reply will be highly appreciated. All the best. Rujing Zha _______________________________________________ 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.
2014/1/5, charujing charujing@gmail.com:
Hi Ruopeng and Zeke, Thanks. I will try the latest version. CentOS has 6.0,6.1,6.2,6.3,6.4 and 6.5, also part of them have desktop, server and alternate version. And in Freesurfer download page we can see: OSPlatformVersionRelease DateDownloadSize LinuxCentOS 6 x86_64 (64b)stable v5.3.015 May 2013freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz4.2G LinuxCentOS 4 x86_64 (64b)stable v5.3.015 May 2013freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0.tar.gz4.0G LinuxCentOS 4 (32b)stable v5.3.015 May 2013freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz3.8G MacLion OX X 10.7 (64b Intel)stable v5.3.015 May 2013freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg3.5G MacSnowLeopard OS X 10.6 (32b Intel)stable v5.3.015 May 2013freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg3.2G VirtualboxXubuntu 12.04stable v5.3.015 Aug 2013freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz9.0G
Also I want to know which CentOS version(6.0,6.1,6.2,6.3,6.4 or 6.5?) and its desktop, alternate or server I should installed or all of them are appropriate for freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz. Thanks Ruopeng and Zeke. All the best. Rujing Zha
2014-01-05
charujing
发件人：zkaufman@nmr.mgh.harvard.edu 发送时间：2014-01-05 07:10 主题：Re: [Freesurfer] problems about freeview 收件人："charujing"charujing@gmail.com 抄送："Ruopeng Wang"rpwang@nmr.mgh.harvard.edu,"freesurfer"freesurfer@nmr.mgh.harvard.edu,"Z K"zkaufman@nmr.mgh.harvard.edu
Hello Rujing,
You can download the most up to date version of freeview using the following link:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/dev/
In order to use this version, you will need to replace the file $FREESURFER_HOME/bin/freeview.bin currently on your system, with the file you download from the link above. Let me know if you need additional assistance.
-Zeke
Hi Rujing,
I am able to replicate the issue with 5.3.0 release. The good news is the
issue does not appear in the current dev version (so I think it has been fixed). Zeke, would it be possible for Rujing to download a copy of the latest freeview build?
Best, Ruopeng
On Jan 4, 2014, at 10:40 AM, "charujing" charujing@gmail.com wrote:
Dear doug, bruce and others, Previously I could not view " freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot
" from the "http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis". The
freeview did represent 3 images. But it reported a something about no geomatric information and I couldnot configure the overlay(When I clicked the "configure overlay", it stopped without any response). My OS
is CentOS 6.5 desktop version, and graphic card is NVIDIA GEFORCE GTX 650 and setup the NVIDIA driver. Freesurfer version is freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz.My computer has
2G memory and 4 processors. I need help to fix it. If anyone have viewed sample data or other data(*.inflated, *sig.cluster.mgh,and *sig.ocn.annot) simultaneously successfully by freeview just as above, would you please tell me some information? The information I need is Freesurer version, Centos version(desktop or others) and something in CentOS setup, graphic card version and its driver, memory size. Thanks very much, doug, brucen and others. Any reply will be highly appreciated. All the best. Rujing Zha _______________________________________________ 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@nmr.mgh.harvard.edu
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charujing -
rujing cha
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Ruopeng Wang -
Z K -
zkaufman＠nmr.mgh.harvard.edu