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
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
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 fischl@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 Zha"charujing123@163.com 抄送："freesurfer"freesurfer@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.
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
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 fischl@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 Zha"charujing123@163.com 抄送："freesurfer"freesurfer@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.
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 fischl@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 Zha"charujing123@163.com 抄送："freesurfer"freesurfer@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%C2%A0 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%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C... rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail.
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 fischl@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 Zha"charujing123@163.com 抄送："freesurfer"freesurfer@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 fischl@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 Zha"charujing123@163.com 抄送："freesurfer"freesurfer@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.
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 fischl@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 Zha"charujing123@163.com 抄送："freesurfer"freesurfer@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 fischl@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 Zha"charujing123@163.com 抄送："freesurfer"freesurfer@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%C2%A0%C2%A0 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%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C...
e
rror but does not contain patient information, please contact the sender and p
ro
perly dispose of the e-mail.
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 fischl@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 Zha"charujing123@163.com 抄送："freesurfer"freesurfer@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 fischl@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 Zha"charujing123@163.com 抄送："freesurfer"freesurfer@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 fischl@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 Zha"charujing123@163.com 抄送："freesurfer"freesurfer@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.
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 fischl@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 Zha"charujing123@163.com 抄送："freesurfer"freesurfer@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 fischl@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 Zha"charujing123@163.com 抄送："freesurfer"freesurfer@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 fischl@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 Zha"charujing123@163.com > 抄送："freesurfer"freesurfer@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%C2%A0%C2%A0%C2%... > > > 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%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C...
?? ?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%C2%A0 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%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C... rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail.
Hi Bruce, Thanks Bruce. I will try the FTP. Would you please help me deal with another two problems? The 1st one is : There is a excellent segmentation in -surfs after editing the pial and running -autorecon-pial. Some voxels was removed from the brainmask.mgz in editing the pial. However the -aseg image still have those voxels which I have removed from the brainmask.mgz. Does this aseg image will influence my group thickness analysis if I donot process additionally? There are brainmask.mgz(pic 1) and aseg(pic 2) snapshots in the attachment. The 2nd one is : I could not visualize the inflated image properly by tksurfer. Here was the detailed describe: tksurfer yizhihui rh inflated I could see little thing in the tksurfer after typing the command above. The result can be got in picture 3 of the attachment and the standard output message can be seen in the picture 4. I had visualized it in the freeview tool by typing "freeview -f $SUBJETCS_DIR/yizhihui/surf/rh.inflated ". The result can be seen in picture 5. CentOS 5.8 is used in my server and I use "freesurfer-Linux-centos4-stable-pib-v5.3.0". Thanks in advance. All the best.
2013-12-17
Rujing Zha
发件人：Bruce Fischl fischl@nmr.mgh.harvard.edu 发送时间：2013-12-16 23:57 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人："Rujing Zha"charujing123@163.com 抄送："freesurfer"freesurfer@nmr.mgh.harvard.edu
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 fischl@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 Zha"charujing123@163.com 抄送："freesurfer"freesurfer@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 fischl@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 Zha"charujing123@163.com 抄送："freesurfer"freesurfer@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 fischl@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 Zha"charujing123@163.com 抄送："freesurfer"freesurfer@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 does not contain patient information, please contact the sender and pro perly dispose of the e-mail.
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 fischl@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 Zha"charujing123@163.com 抄送："freesurfer"freesurfer@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
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 greve@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："freesurfer"freesurfer@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 fischl@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 Zha"charujing123@163.com 抄送："freesurfer"freesurfer@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 greve@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
Is that all it says? Can you send the log file?
On 12/16/2013 10:00 PM, Rujing Zha wrote:
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 greve@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：*"freesurfer"freesurfer@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 fischl@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 Zha"charujing123@163.com 抄 送："freesurfer"freesurfer@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 greve@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
Dear Doug, Thanks for your kindhearted help, Doug. I upload the standard output and error message file named "unpack_log", and the unpack log file named unpack.log in the attachment. Thanks in advance. All the best.
2013-12-18
Rujing Zha
发件人：Douglas N Greve greve@nmr.mgh.harvard.edu 发送时间：2013-12-18 00:51 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人："Rujing Zha"charujing123@163.com 抄送："freesurfer"freesurfer@nmr.mgh.harvard.edu
Is that all it says? Can you send the log file?
On 12/16/2013 10:00 PM, Rujing Zha wrote:
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 greve@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：*"freesurfer"freesurfer@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 fischl@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 Zha"charujing123@163.com 抄 送："freesurfer"freesurfer@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 greve@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 greve@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
There are lots of warnings in the log file. Have you anonymized this data or done anything to the DICOM files since they came from the scanner?
On 12/18/2013 03:44 AM, Rujing Zha wrote:
Dear Doug, Thanks for your kindhearted help, Doug. I upload the standard output and error message file named "unpack_log", and the unpack log file named unpack.log in the attachment. Thanks in advance. All the best. 2013-12-18
/Rujing Zha/
*发件人：*Douglas N Greve greve@nmr.mgh.harvard.edu *发送时间：*2013-12-18 00:51 *主题：*Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR *收件人：*"Rujing Zha"charujing123@163.com *抄送：*"freesurfer"freesurfer@nmr.mgh.harvard.edu Is that all it says? Can you send the log file? On 12/16/2013 10:00 PM, Rujing Zha wrote:
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 greve@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：*"freesurfer"freesurfer@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 fischl@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 Zha"charujing123@163.com 抄 送："freesurfer"freesurfer@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 greve@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 greve@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
Hi Doug, Doug, it's very kind of you to help me all the time. Thanks. I didnot do anything except move all DICOM files into one folder which is the same as other subjects. According your prompt, I checked the DICOM and found that this subjects have two 3d imag. And I separated the data into 2 folders. So the recon-all running normally. Thanks Doug. All the best.
2013-12-19
Rujing Zha
发件人：Douglas N Greve greve@nmr.mgh.harvard.edu 发送时间：2013-12-19 04:48 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人："Rujing Zha"charujing123@163.com 抄送："freesurfer"freesurfer@nmr.mgh.harvard.edu
There are lots of warnings in the log file. Have you anonymized this data or done anything to the DICOM files since they came from the scanner?
On 12/18/2013 03:44 AM, Rujing Zha wrote:
Dear Doug, Thanks for your kindhearted help, Doug. I upload the standard output and error message file named "unpack_log", and the unpack log file named unpack.log in the attachment. Thanks in advance. All the best. 2013-12-18
/Rujing Zha/
*发件人：*Douglas N Greve greve@nmr.mgh.harvard.edu *发送时间：*2013-12-18 00:51 *主题：*Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR *收件人：*"Rujing Zha"charujing123@163.com *抄送：*"freesurfer"freesurfer@nmr.mgh.harvard.edu Is that all it says? Can you send the log file? On 12/16/2013 10:00 PM, Rujing Zha wrote:
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 greve@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：*"freesurfer"freesurfer@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 fischl@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 Zha"charujing123@163.com 抄 送："freesurfer"freesurfer@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
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