Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR
Hi Rujing why does the input volume have multiple frames? Is it a multi-echo dataset? cheers Bruce On Sat, 14 Dec 2013, Rujing Zha wrote: Hi Bruce, It generated a 013 subfolder in after running this code unpacksdcmdir -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3danat mgz 001.mgz. It is 15 that I can see the number of t1_mpr_ns_sag_iso_zhang in the unpack.log. Then I ran recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liujunhao, and it finished without error. recon-all -s liujunhao -all was run and ERROR would be displayed: ERROR: input(s) cannot have multiple frames! The recon-all.log unpack.log and scan.info were unloaded in the attachment. Thanks. All the best. 2013-12-14 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.
Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR
Hi Bruce, I saw the scan.info, and the 13 line is functional image which has a 6 number. I guess this is why recon-all report the multiple frames. Would you please tell me how I can deal with this problem which unpacksdcmdir recognize the number 13 not 15? Thanks. All the best. 2013-12-16 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 21:54 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing why does the input volume have multiple frames? Is it a multi-echo dataset? cheers Bruce On Sat, 14 Dec 2013, Rujing Zha wrote: Hi Bruce, It generated a 013 subfolder in after running this code unpacksdcmdir -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3danat mgz 001.mgz. It is 15 that I can see the number of t1_mpr_ns_sag_iso_zhang in the unpack.log. Then I ran recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liujunhao, and it finished without error. recon-all -s liujunhao -all was run and ERROR would be displayed: ERROR: input(s) cannot have multiple frames! The recon-all.log unpack.log and scan.info were unloaded in the attachment. Thanks. All the best. 2013-12-14 Rujing Zha 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] unpacksdcmdir: specifies unpacking rules from the command-line ERROR
but why are you giving recon-all the path to run 013 instead of 015? I don't know the fsfast file structure, but your scan.info says that 013 is an EPI fun and 015 is the mprage On Sat, 14 Dec 2013, Rujing Zha wrote: Hi Bruce, It generated a 013 subfolder in after running this code unpacksdcmdir -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3danat mgz 001.mgz. It is 15 that I can see the number of t1_mpr_ns_sag_iso_zhang in the unpack.log. Then I ran recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liujunhao, and it finished without error. recon-all -s liujunhao -all was run and ERROR would be displayed: ERROR: input(s) cannot have multiple frames! The recon-all.log unpack.log and scan.info were unloaded in the attachment. Thanks. All the best. 2013-12-14 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.
Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR
Dear Bruce, I did setup the -run 015 not 013 in unpacksdcmdir as I told in previous message. But it generated the 013 folder automatically after running unpacksdcdir, which made me so confused. As it created the 013 folder, I guess unpacksdcmdir didnot recognized structure image correctly which was in the 15th line of the scan.info. Thanks Bruce. All the best. 2013-12-16 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:12 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu but why are you giving recon-all the path to run 013 instead of 015? I don't know the fsfast file structure, but your scan.info says that 013 is an EPI fun and 015 is the mprage On Sat, 14 Dec 2013, Rujing Zha wrote: Hi Bruce, It generated a 013 subfolder in after running this code unpacksdcmdir -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3danat mgz 001.mgz. It is 15 that I can see the number of t1_mpr_ns_sag_iso_zhang in the unpack.log. Then I ran recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liujunhao, and it finished without error. recon-all -s liujunhao -all was run and ERROR would be displayed: ERROR: input(s) cannot have multiple frames! The recon-all.log unpack.log and scan.info were unloaded in the attachment. Thanks. All the best. 2013-12-14 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 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] unpacksdcmdir: specifies unpacking rules from the command-line ERROR
sorry, I don't know that code very well. Doug is probably the right one to help you Bruce On Mon, 16 Dec 2013, Rujing Zha wrote: Dear Bruce, I did setup the -run 015 not 013 in unpacksdcmdir as I told in previous message. But it generated the 013 folder automatically after running unpacksdcdir, which made me so confused. As it created the 013 folder, I guess unpacksdcmdir didnot recognized structure image correctly which was in the 15th line of the scan.info. Thanks Bruce. All the best. 2013-12-16 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:12 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu but why are you giving recon-all the path to run 013 instead of 015? I don't know the fsfast file structure, but your scan.info says that 013 is ?? ?an EPI fun and 015 is the mprage On Sat, 14 Dec 2013, Rujing Zha wrote: Hi Bruce, It generated a 013 subfolder in after running this code unpacksdcmdir -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3danat mg z 001.mgz. It is 15 that I can see the number of t1_mpr_ns_sag_iso_zhang ?? ?in the unpack.log. Then I ran recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liujunha o, and it finished without error. recon-all -s liujunhao -all was run and ERROR would be displayed: ERROR: input(s) cannot have multiple frames! The recon-all.log unpack.log and scan.info were unloaded in the attachmen t. Thanks. All the best. 2013-12-14 _ ___ 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 i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly 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] unpacksdcmdir: specifies unpacking rules from the command-line ERROR
Dear Bruce, Thanks Bruce. That's all right. I want to know if I e-mail to you my subject's data successfully. The subject's image had a incorrect segmentation in surfs after recon-all. Thanks in advance. All the best. 2013-12-16 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:24 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu sorry, I don't know that code very well. Doug is probably the right one to help you Bruce On Mon, 16 Dec 2013, Rujing Zha wrote: Dear Bruce, I did setup the -run 015 not 013 in unpacksdcmdir as I told in previous message. But it generated the 013 folder automatically after running unpacksdcdir, which made me so confused. As it created the 013 folder, I guess unpacksdcmdir didnot recognized structure image correctly which was in the 15th line of the scan.info. Thanks Bruce. All the best. 2013-12-16 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:12 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu but why are you giving recon-all the path to run 013 instead of 015? I don't know the fsfast file structure, but your scan.info says that 013 is ?? ?an EPI fun and 015 is the mprage On Sat, 14 Dec 2013, Rujing Zha wrote: Hi Bruce, It generated a 013 subfolder in after running this code unpacksdcmdir -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3danat mg z 001.mgz. It is 15 that I can see the number of t1_mpr_ns_sag_iso_zhang ?? ?in the unpack.log. Then I ran recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liujunha o, and it finished without error. recon-all -s liujunhao -all was run and ERROR would be displayed: ERROR: input(s) cannot have multiple frames! The recon-all.log unpack.log and scan.info were unloaded in the attachmen t. Thanks. All the best. 2013-12-14 _ ___ 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 i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly 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] unpacksdcmdir: specifies unpacking rules from the command-line ERROR
no, I didn't get it On Mon, 16 Dec 2013, Rujing Zha wrote: Dear Bruce, Thanks Bruce. That's all right. I want to know if I e-mail to you my subject's data successfully. The subject's image had a incorrect segmentation in surfs after recon-all. Thanks in advance. All the best. 2013-12-16 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:24 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu sorry, I don't know that code very well. Doug is probably the right one to ?? ? help you Bruce On Mon, 16 Dec 2013, Rujing Zha wrote: Dear Bruce, I did setup the -run 015 not 013 in unpacksdcmdir as I told in previo us message. But it generated the 013 folder automatically after running unpacksdcdir, which made me so confused. As it created the 013 folder, I guess unpacksdcmdir didnot recognized structure image correctly which was in the 15th line of the scan.info. ?? ? Thanks Bruce. All the best. 2013-12-16 _ ___ Rujing Zha _ ___ 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:12 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the ?? ? command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu but why are you giving recon-all the path to run 013 instead of 015? I ?? ? don't know the fsfast file structure, but your scan.info says that 013 is ?? ?an EPI fun and 015 is the mprage On Sat, 14 Dec 2013, Rujing Zha wrote: Hi Bruce, It generated a 013 subfolder in after running this code unpacksdcmdir ?? ? -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3danat ?? ?mg z 001.mgz. It is 15 that I can see the number of t1_mpr_ns_sag_iso_zhan g ?? ?in the unpack.log. Then I ran recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liujun ha o, and it finished without error. recon-all -s liujunhao -all was run and ERROR would be displayed: ERROR: input(s) cannot have multiple frames! The recon-all.log unpack.log and scan.info were unloaded in the attachm en t. Thanks. All the best. 2013-12-14 ___ __ ___ 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 i s addressed. If you believe this e-mail was sent to you in error and the e- ma il contains patient information, please contact the Partners Compliance Help Li ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and p ro perly 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] how to do regression rather than group comparison in freesurfer
Yes. Sorry, I should mention this: the data is DTI (FA maps) from FSL. Can I still use the same methods? Hi Jacky, have you looked at the group analysis tutorial? It includes instructions on how to include age as a continuous covariate. doug On 12/12/2013 06:28 PM, r...@nmr.mgh.harvard.edu wrote: Dear All, Does anyone know how to run regression (with covariates of interest) in freesurfer. I know people usually do group comparison but I need to do regression with a continuous variable. Or do I have to use SPM? Cheers, Jacky ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR
Hi Bruce, Maybe 163 email has some problems. I will try my gmail to send you and Louis my data. But I donot know whether your email can get attachment size 289M? Thanks. All the best. 2013-12-16 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:37 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu no, I didn't get it On Mon, 16 Dec 2013, Rujing Zha wrote: Dear Bruce, Thanks Bruce. That's all right. I want to know if I e-mail to you my subject's data successfully. The subject's image had a incorrect segmentation in surfs after recon-all. Thanks in advance. All the best. 2013-12-16 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:24 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu sorry, I don't know that code very well. Doug is probably the right one to ?? ? help you Bruce On Mon, 16 Dec 2013, Rujing Zha wrote: Dear Bruce, I did setup the -run 015 not 013 in unpacksdcmdir as I told in previo us message. But it generated the 013 folder automatically after running unpacksdcdir, which made me so confused. As it created the 013 folder, I guess unpacksdcmdir didnot recognized structure image correctly which was in the 15th line of the scan.info. ?? ? Thanks Bruce. All the best. 2013-12-16 _ ___ Rujing Zha _ ___ 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:12 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the ?? ? command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu but why are you giving recon-all the path to run 013 instead of 015? I ?? ? don't know the fsfast file structure, but your scan.info says that 013 is ?? ?an EPI fun and 015 is the mprage On Sat, 14 Dec 2013, Rujing Zha wrote: Hi Bruce, It generated a 013 subfolder in after running this code unpacksdcmdir ?? ? -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3danat ?? ?mg z 001.mgz. It is 15 that I can see the number of t1_mpr_ns_sag_iso_zhan g ?? ?in the unpack.log. Then I ran recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liujun ha o, and it finished without error. recon-all -s liujunhao -all was run and ERROR would be displayed: ERROR: input(s) cannot have multiple frames! The recon-all.log unpack.log and scan.info were unloaded in the attachm en t. Thanks. All the best. 2013-12-14 ___ __ ___ 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 i s addressed. If you believe this e-mail was sent to you in error and the e- ma il contains patient information, please contact the Partners Compliance Help Li ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and p ro perly 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. ___ 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
Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR
Hi Rujing you can use either our FTP site or our file drop. Info for this is at http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange and https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html cheers Bruce On Mon, 16 Dec 2013, Rujing Zha wrote: Hi Bruce, Maybe 163 email has some problems. I will try my gmail to send you and Louis my data. But I donot know whether your email can get attachment size 289M? Thanks. All the best. 2013-12-16 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:37 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu no, I didn't get it On Mon, 16 Dec 2013, Rujing Zha wrote: Dear Bruce, Thanks Bruce. That's all right. I want to know if I e-mail to you my subject's data successfully. The subject's image had a incorrect segmentation in surfs after recon-all. Thanks in advance. All the best. 2013-12-16 _ ___ Rujing Zha _ ___ 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:24 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the ?? ? command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu sorry, I don't know that code very well. Doug is probably the right one t o ?? ? help you Bruce On Mon, 16 Dec 2013, Rujing Zha wrote: Dear Bruce, I did setup the -run 015 not 013 in unpacksdcmdir as I told in prev io us message. But it generated the 013 folder automatically after running ?? ? unpacksdcdir, which made me so confused. As it created the 013 folder, I guess unpacksdcmdir didnot recognized structure image correctly which was in the 15th line of the scan.info . ?? ? Thanks Bruce. All the best. 2013-12-16 ___ __ ___ Rujing Zha ___ __ ___ 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:12 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from th e ?? ? command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu but why are you giving recon-all the path to run 013 instead of 015? I ?? ? ?? ? don't know the fsfast file structure, but your scan.info says that 01 3 is ?? ?an EPI fun and 015 is the mprage On Sat, 14 Dec 2013, Rujing Zha wrote: Hi Bruce, It generated a 013 subfolder in after running this code unpacksdcmdi r ?? ? -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3dana t ?? ?mg z 001.mgz. It is 15 that I can see the number of t1_mpr_ns_sag_iso_zh an g ?? ?in the unpack.log. Then I ran recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liuj un ha o, and it finished without error. recon-all -s liujunhao -all was run and ERROR would be displayed: ?? ? ERROR: input(s) cannot have multiple frames! The recon-all.log unpack.log and scan.info were unloaded in the attac hm en t. Thanks. All the best. 2013-12-14 _ __ __ ___ 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 i s addressed. If you believe this e-mail was sent to you in error and the ?? ?e- ma il contains patient information, please contact the Partners Compliance He lp Li ne at http://www.partners.org/complianceline . If the e-mail was sent to you ?? ?in e rror but does not contain patient information, please contact the sender and p ro perly 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 i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but
Re: [Freesurfer] how to do regression rather than group comparison in freesurfer
yes, no problem On 12/16/2013 10:13 AM, r...@nmr.mgh.harvard.edu wrote: Yes. Sorry, I should mention this: the data is DTI (FA maps) from FSL. Can I still use the same methods? Hi Jacky, have you looked at the group analysis tutorial? It includes instructions on how to include age as a continuous covariate. doug On 12/12/2013 06:28 PM, r...@nmr.mgh.harvard.edu wrote: Dear All, Does anyone know how to run regression (with covariates of interest) in freesurfer. I know people usually do group comparison but I need to do regression with a continuous variable. Or do I have to use SPM? Cheers, Jacky ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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] unpacksdcmdir: specifies unpacking rules from the command-line ERROR
If you passed -run 015 it should have generated a 015 folder and not a 013 folder. The only thing I can think may have gone wrong is that it expected 15 instead of 015. doug On 12/16/2013 09:24 AM, Bruce Fischl wrote: sorry, I don't know that code very well. Doug is probably the right one to help you Bruce On Mon, 16 Dec 2013, Rujing Zha wrote: Dear Bruce, I did setup the -run 015 not 013 in unpacksdcmdir as I told in previous message. But it generated the 013 folder automatically after running unpacksdcdir, which made me so confused. As it created the 013 folder, I guess unpacksdcmdir didnot recognized structure image correctly which was in the 15th line of the scan.info. Thanks Bruce. All the best. 2013-12-16 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:12 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu but why are you giving recon-all the path to run 013 instead of 015? I don't know the fsfast file structure, but your scan.info says that 013 is ?? ?an EPI fun and 015 is the mprage On Sat, 14 Dec 2013, Rujing Zha wrote: Hi Bruce, It generated a 013 subfolder in after running this code unpacksdcmdir -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3danat mg z 001.mgz. It is 15 that I can see the number of t1_mpr_ns_sag_iso_zhang ?? ?in the unpack.log. Then I ran recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liujunha o, and it finished without error. recon-all -s liujunhao -all was run and ERROR would be displayed: ERROR: input(s) cannot have multiple frames! The recon-all.log unpack.log and scan.info were unloaded in the attachmen t. Thanks. All the best. 2013-12-14 _ ___ 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 i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] problem creating annotation using mri_sample_parc?
Dear Bruce or someone else, would you mind answering a little more in detail, please? I am stuck. There is hardly any thread about the command mris_sample_parc, but I need this function. 1) This file called cma_parcellation_colors.txt, is an option for mris_sample_parc. Where does that file come from? How am I supposed to create it? 2) What is missing if the loading of the created annotation file onto a surface (in freeview) gives the following error, repeating for infinity CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory What does this error mean, at all? Thank you and please excuse my insisting! Markus 2013/12/14 Markus Gschwind markus.gschw...@gmail.com Thank you Bruce, I read that mris_sample_parc samples a volumetric parcellation onto a surface. I understand that this is like creating from a file of the type of aseg a corresponding file of the type of aparc.annot.ctab. Is this not true? Do I actually have to create the aparc.annot.ctab type file manually and give this as the above mentionned file to the command? The file is only an optional arguement though? Thanks again, Markus 2013/12/14 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Markus you need to create that file (or update FreeSurferColorLUT.txt) to reflect whatever you have in /Documents/myROIfile.mgz cheers Bruce On Sat, 14 Dec 2013, Markus Gschwind wrote: Dear Bruce, Thank you for your answer. I have not yet gotten it correctly. 1) Where does that file come from? Should I create it? how? 2) what is missing in the command of mris_sample_parc? Why does it now work? 3) what does the second error mean? CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory Thanks in advance! [cleardot.gif] Markus 2013/12/13 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Markus that file translates indices/annotations into colors to display and human reasable names. cheers Bruce On Fri, 13 Dec 2013, Markus Gschwind wrote: I can precise the question, actually there are three: 1) ist the command correct? mris_sample_parc -v -sdir subject001 rh ~/Documents/myROIfile.mgz rh.myROIfile.annot 2) I do not understand the meaning of this claimed file cma_parcellation_colors.txt Actually this does not exist. In the Wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/mris_sample_parc) it says that there was an optional arguement -file filename use filename as translation (default: 'cma_parcellation_colors.txt') If I understand correctly, translation points ot a problem of different spaces, but the filename rather seems something like a parcellation/atlas color table? 3) The result of this problem seems to be that I cannot annotate the surface using the created annotation file. It gives this error, which i do not understand. CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory ... etc. Can anyone help me find the problem? Thank you in advance! Markus 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
[Freesurfer] Generating list of subjects: a tcsh scripting problem
Hello, I am having a tcsh scripting problem for generating a text file containing the list of subjects, and I would appreciate any help. I've explained my problem here: http://stackoverflow.com/q/20617206/2769441 All the best, Emad ___ 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] Generating list of subjects: a tcsh scripting problem
Hello Emad, Considering your output when you run this from the source command generates only the first subject in your list, I would check to see if there is a looping issue. Because you are no longer within the same directory as when you ran it from the terminal, the script may not be returning to the same homedir. I would add in a CD command as the last line of your for loop and see if that fixed the problem. I hope this helps, Jacob Hello, I am having a tcsh scripting problem for generating a text file containing the list of subjects, and I would appreciate any help. I've explained my problem here: http://stackoverflow.com/q/20617206/2769441 All the best, Emad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
Re: [Freesurfer] problem creating annotation using mri_sample_parc?
Hi Markus for example, this is what is in the one we use: mris_info $FREESURFER_HOME/average/lh.destrieux.simple.2009-07-29.gcs reading color table from GCSA file average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized GCSA file /cluster/p41/fischl/dev/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs opened 0 Unknown 0 0 00 1 G_and_S_frontomargin 23 220 600 2 G_and_S_occipital_inf23 60 1800 3 G_and_S_paracentral 63 100 600 4 G_and_S_subcentral 63 20 2200 5 G_and_S_transv_frontopol 13 0 2500 6 G_and_S_cingul-Ant 26 60 00 7 G_and_S_cingul-Mid-Ant 26 60 750 8 G_and_S_cingul-Mid-Post 26 60 1500 . . . it translates between an index (e.g. 1), a human readable name (G_and_S_frontomargin) and an rgb value for displaying on the surface (23 220 60). You would have the indices in your volume, then this color table would translate it into values to display on the surface. Make sense? Bruce On Mon, 16 Dec 2013, Markus Gschwind wrote: Dear Bruce or someone else, would you mind answering a little more in detail, please? I am stuck. There is hardly any thread about the command mris_sample_parc, but I need this function. 1) This file called cma_parcellation_colors.txt, is an option for mris_sample_parc. Where does that file come from? How am I supposed to create it? 2) What is missing if the loading of the created annotation file onto a surface (in freeview) gives the following error, repeating for infinity CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory What does this error mean, at all? Thank you and please excuse my insisting! Markus 2013/12/14 Markus Gschwind markus.gschw...@gmail.com Thank you Bruce, I read that mris_sample_parc samples a volumetric parcellation onto a surface. I understand that this is like creating from a file of the type of aseg a corresponding file of the type of aparc.annot.ctab. Is this not true? Do I actually have to create the aparc.annot.ctab type file manually and give this as the above mentionned file to the command? The file is only an optional arguement though? Thanks again, Markus 2013/12/14 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Markus you need to create that file (or update FreeSurferColorLUT.txt) to reflect whatever you have in /Documents/myROIfile.mgz cheers Bruce On Sat, 14 Dec 2013, Markus Gschwind wrote: Dear Bruce, Thank you for your answer. I have not yet gotten it correctly. 1) Where does that file come from? Should I create it? how? 2) what is missing in the command of mris_sample_parc? Why does it now work? 3) what does the second error mean? CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory Thanks in advance! [cleardot.gif] Markus 2013/12/13 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Markus that file translates indices/annotations into colors to display and human reasable names. cheers Bruce On Fri, 13 Dec 2013, Markus Gschwind wrote: I can precise the question, actually there are three: 1) ist the command correct? mris_sample_parc -v -sdir subject001 rh ~/Documents/myROIfile.mgz rh.myROIfile.annot 2) I do not understand the meaning of this claimed file cma_parcellation_colors.txt Actually this does not exist. In the Wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/mris_sample_parc) it says that there was an optional arguement -file filename use filename as translation (default: 'cma_parcellation_colors.txt') If I understand correctly, translation points ot a problem of different spaces, but the filename rather seems something like a parcellation/atlas color table? 3) The result of this problem seems to be that I cannot annotate the surface using the created annotation file. It gives this error, which i do not understand. CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory
Re: [Freesurfer] qdec analysis with 2 covariates
Hi Doug I ran : mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 2.0 abs --cwp .9 I have attached three of the output summary files Can you please confirm how to assess the cluster-wise p-value? Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 12:12:01 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates I would have thought that it would have gotten all of them. You can try something like --cwp .9 On 12/13/2013 01:03 PM, Jon Wieser wrote: HI doug thanks, that worked. it captured from 3-13 clusters for each contrast, not quite the 30-45 that I was seeing in the GUI. perhaps theses are the most significant clusters? Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 11:43:29 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates use the command I gave you before just add --cwp .99 to it doug On 12/13/2013 12:25 PM, Jon Wieser wrote: Hi doug it's requesting the --sim option mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 ERROR: must spec --sim mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 --sim ERROR: flag --sim requires four arguments what args do I give the --sim! Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 11:18:49 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates sorry, it is --cwp On 12/13/2013 12:12 PM, Jon Wieser wrote: HI Doug MRI_glmfit-sim didn't recognize the --cwd option mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99 ERROR: Flag --cwd unrecognized. --glmdir MTA_ADHD_MJ --cwd .99 - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 10:54:19 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates I'm sure that those clusters are not very significant. Try running mri_glmfit-sim with --cwd .99 to capture all clusters doug On 12/12/2013 03:27 PM, Jon Wieser wrote: HI Doug, here's a screen shot, showing the clusters and a scatter plot for one of the 45 clusters. for this dataset, ussualy there is 0 or 1 clusters after monte carlo simulation. i'm not sure if they match one of the 45 clusters in qdec. i'l have to look into that. I would like to have a file which contains the data represented in the scatter plot, for all of the 45 clusters, vlaues of thickness for each subject. is that possible? I tried runnin mri_surfcluster, but it only gave me the average data for that clusters, not the individual data. thanks! Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Thursday, December 12, 2013 1:15:58 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates I'm not sure what is going on. Can you send a screen shot of the qdec window when you see 40 clusters? It might be that it is showing clusters regardless of the cluster significance. Do the 3 or 4 clusters created when you run mri_glmfit-sim match clusters in qdec? On 12/10/2013 05:32 PM, Jon Wieser wrote: Hi Doug I'm looking at the effect of MJ usage, the effect of whetherthe subject has AHDH, and the interaction between MJ usage and ADHD our threshold is 1.3 i have attahced our qdec.table.dat file we are also looking at age and gender as covariates Jon Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 4:20:30 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates which contrast are you looking at in QDEC? Also, what is the voxel-wise threshold in QDEC? The value I gave in the command below is 1.3 but I got that from one of your CSD files. On 12/10/2013 05:10 PM, Jon Wieser wrote: HI doug, no, the summary files in the contrasts have the same # of cluster as the columns in their OCN.dat \ the 40 cluster are seen in qdec when I run the find cluster and Goto max button. most of these clusters go away in qdec when I run the montecarlo simulation Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 4:03:06 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates So one of the contrasts has 40 clusters in the summary file but the y.ocn.dat file only has a few columns? On
Re: [Freesurfer] Output of recon-all -all -openmp 8 does not show brainmask.mgz
Pablo, I need the recon-all.log file located in the $SUBJECTS_DIR/scripts directory. Sorry for the confusion. -Zeke On 12/13/2013 04:48 PM, pablo najt wrote: Dear Zeke, Thank you so much. As I am not sure which is the log file that we use I am attaching mri_nu (in mri directory) and talairach_avi (in mri/transformations directory). Thanks, Pablo Date: Fri, 13 Dec 2013 16:21:48 -0500 From: zkauf...@nmr.mgh.harvard.edu To: pablon...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Output of recon-all -all -openmp 8 does not show brainmask.mgz Hello Pablo, Please send me the recon-all.log file for the subject and I will take a look. -Zeke On 12/13/2013 03:41 PM, pablo najt wrote: Dear FS, I am checking on the outputs of recon-all -all using the flag -openmp 8. As I did with standard recon-all -all comand line I was trying to check brainmask.mgz, but there is not such file. Is there anything wrong with my outputs? Or I should be checking a different file? Thank you, Pablo ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] qdec analysis with 2 covariates
look at the CWP column doug On 12/16/2013 05:14 PM, Jon Wieser wrote: Hi Doug I ran : mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 2.0 abs --cwp .9 I have attached three of the output summary files Can you please confirm how to assess the cluster-wise p-value? Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 12:12:01 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates I would have thought that it would have gotten all of them. You can try something like --cwp .9 On 12/13/2013 01:03 PM, Jon Wieser wrote: HI doug thanks, that worked. it captured from 3-13 clusters for each contrast, not quite the 30-45 that I was seeing in the GUI. perhaps theses are the most significant clusters? Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 11:43:29 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates use the command I gave you before just add --cwp .99 to it doug On 12/13/2013 12:25 PM, Jon Wieser wrote: Hi doug it's requesting the --sim option mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 ERROR: must spec --sim mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 --sim ERROR: flag --sim requires four arguments what args do I give the --sim! Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 11:18:49 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates sorry, it is --cwp On 12/13/2013 12:12 PM, Jon Wieser wrote: HI Doug MRI_glmfit-sim didn't recognize the --cwd option mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99 ERROR: Flag --cwd unrecognized. --glmdir MTA_ADHD_MJ --cwd .99 - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 10:54:19 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates I'm sure that those clusters are not very significant. Try running mri_glmfit-sim with --cwd .99 to capture all clusters doug On 12/12/2013 03:27 PM, Jon Wieser wrote: HI Doug, here's a screen shot, showing the clusters and a scatter plot for one of the 45 clusters. for this dataset, ussualy there is 0 or 1 clusters after monte carlo simulation. i'm not sure if they match one of the 45 clusters in qdec. i'l have to look into that. I would like to have a file which contains the data represented in the scatter plot, for all of the 45 clusters, vlaues of thickness for each subject. is that possible? I tried runnin mri_surfcluster, but it only gave me the average data for that clusters, not the individual data. thanks! Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Thursday, December 12, 2013 1:15:58 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates I'm not sure what is going on. Can you send a screen shot of the qdec window when you see 40 clusters? It might be that it is showing clusters regardless of the cluster significance. Do the 3 or 4 clusters created when you run mri_glmfit-sim match clusters in qdec? On 12/10/2013 05:32 PM, Jon Wieser wrote: Hi Doug I'm looking at the effect of MJ usage, the effect of whetherthe subject has AHDH, and the interaction between MJ usage and ADHD our threshold is 1.3 i have attahced our qdec.table.dat file we are also looking at age and gender as covariates Jon Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 4:20:30 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates which contrast are you looking at in QDEC? Also, what is the voxel-wise threshold in QDEC? The value I gave in the command below is 1.3 but I got that from one of your CSD files. On 12/10/2013 05:10 PM, Jon Wieser wrote: HI doug, no, the summary files in the contrasts have the same # of cluster as the columns in their OCN.dat \ the 40 cluster are seen in qdec when I run the find cluster and Goto max button. most of these clusters go away in qdec when I run the montecarlo simulation Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 4:03:06 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates So one of the contrasts has 40
Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR
Hi Doug, Thanks Doug. I tried the -run 15 option, it generate a 015 folder. However unpacksdcmdir code echo ERROR message: ERROR:mri_convert child killed: segmentation violation , and the script terminated. All the best. 2013-12-17 Rujing Zha 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 发送时间：2013-12-17 02:56 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： If you passed -run 015 it should have generated a 015 folder and not a 013 folder. The only thing I can think may have gone wrong is that it expected 15 instead of 015. doug On 12/16/2013 09:24 AM, Bruce Fischl wrote: sorry, I don't know that code very well. Doug is probably the right one to help you Bruce On Mon, 16 Dec 2013, Rujing Zha wrote: Dear Bruce, I did setup the -run 015 not 013 in unpacksdcmdir as I told in previous message. But it generated the 013 folder automatically after running unpacksdcdir, which made me so confused. As it created the 013 folder, I guess unpacksdcmdir didnot recognized structure image correctly which was in the 15th line of the scan.info. Thanks Bruce. All the best. 2013-12-16 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:12 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu but why are you giving recon-all the path to run 013 instead of 015? I don't know the fsfast file structure, but your scan.info says that 013 is ?? ?an EPI fun and 015 is the mprage On Sat, 14 Dec 2013, Rujing Zha wrote: Hi Bruce, It generated a 013 subfolder in after running this code unpacksdcmdir -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3danat mg z 001.mgz. It is 15 that I can see the number of t1_mpr_ns_sag_iso_zhang ?? ?in the unpack.log. Then I ran recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liujunha o, and it finished without error. recon-all -s liujunhao -all was run and ERROR would be displayed: ERROR: input(s) cannot have multiple frames! The recon-all.log unpack.log and scan.info were unloaded in the attachmen t. Thanks. All the best. 2013-12-14 _ ___ 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 i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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] design matrix and contrast in fsgdf
Dear all, I want to design a group t-test analysis and correlation analysis for pial thickness. I have read the PPT of freesurfer.groupanalysis, and I wrote a specific design matrix and contrast for my data. However it is the first time that I design matrix in fsgdf by freesurfer. I didnot confirm whether I wrote is correct. I need someone to help me review it. I have two groups, four groups were classified as sex.(Is this necessary or correct?) Here is my design matrix in fsgdf for 2 group t-test: GroupDescriptorFile 1 Title lh_ttest Class con_male Class con_female Class pat_male Class pat_female Variables Ageedu Input subjid1 con_male 1910 Input subjid2 con_male 2020 Input subjid3 con_male 2020 Input subjid4 con_male 1910 Input subjid5 con_female 20 20 Input subjid6 con_female 2020 Input subjid7 con_female 1910 Input subjid8 pat_male 2020 Input subjid9 pat_male 2020 Input subjid10 pat_male 1910 Input subjid11 pat_female 2020 Input subjid12 pat_female 2020 DefaultVariable Age In this section, I just want to compare the patient group(class 3 and 4) and control group(class 1 and 2) in thickness controling the age and education by ANCOVA. Does this fsgdf implement ANCOVA? Here is my contrast for this: 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 Here is my design matrix in fsgdf for partial regression: GroupDescriptorFile 1 Title lh_regression Class con_male Class con_female Class pat_male Class pat_female Variables Ageedu score1 score2 Input subjid1 con_male 1910 2030 Input subjid2 con_male 2020 2030 Input subjid3 con_male 2020 2030 Input subjid4 con_male 1910 2030 Input subjid5 con_female 20 20 2030 Input subjid6 con_female 2020 2030 Input subjid7 con_female 1910 2030 Input subjid8 pat_male 2020 2030 Input subjid9 pat_male 2020 2030 Input subjid10 pat_male 1910 2030 Input subjid11 pat_female 2020 2030 Input subjid12 pat_female 20202030 DefaultVariable score1 In this section, I want to implement partial regression analysis(i.e. score1 and score2) by controling the age,edu and sex. Here is my contrast for score1: 0 0 0 0 0 0 0 0 0 0 0 0 0.25 0.25 0.25 0.25 0 0 0 0 Here is my contrast for score2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.25 0.25 0.25 0.25 Any reply will be highly appreciated. Thanks. All the best. 2013-12-17 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.
