Dear all,
I have T1 images collected from the 7T MRI scanner.
I downloaded the most recent freesurfer software, and followed all instructions to install the software before using it.
I would like to segment the T1 data using its high resolution image, and also to segment the hippocampal subfields.
For command, I use this:
recon-all -all -s <subject name> -hires -i <subject dicom T1 image frame 1 location>
However, I get an error message:
cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca
I'm not sure what I did wrong.
Also, how can I combine high resolution segmentation and hippocampal subfields segmentation?
Could someone please help?
Thanks.
Best regards, Hweeling
Hi Hweeling
what is FREESURFER_HOME set to in the environment? Does that file exist? It is a standard part of our distribution
cheers Bruce
On Tue, 21 Nov 2017, Hwee Ling Lee wrote:
Dear all,
I have T1 images collected from the 7T MRI scanner.
I downloaded the most recent freesurfer software, and followed all instructions to install the software before using it.
I would like to segment the T1 data using its high resolution image, and also to segment the hippocampal subfields.
For command, I use this:
recon-all -all -s <subject name> -hires -i <subject dicom T1 image frame 1 location>
However, I get an error message:
cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca
I'm not sure what I did wrong.
Also, how can I combine high resolution segmentation and hippocampal subfields segmentation?
Could someone please help?
Thanks.
Best regards, Hweeling
Dear Bruce,
Thanks for your reply. I checked the folder and did not find the file that was requested.
What I have in the average folder that has 'RB*.gca' are 'RB_all_2016-05-10.vc700.gca' and 'RB_all_withskull_2016-05-10.vc700.gca'. The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'.
Cheers, Hweeling
On Nov 21, 2017 18:05, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Hweeling
what is FREESURFER_HOME set to in the environment? Does that file exist? It is a standard part of our distribution
cheers Bruce
On Tue, 21 Nov 2017, Hwee Ling Lee wrote:
Dear all,
I have T1 images collected from the 7T MRI scanner.
I downloaded the most recent freesurfer software, and followed all instructions to install the software before using it.
I would like to segment the T1 data using its high resolution image, and also to segment the hippocampal subfields.
For command, I use this:
recon-all -all -s <subject name> -hires -i <subject dicom T1 image frame 1 location>
However, I get an error message:
cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca
I'm not sure what I did wrong.
Also, how can I combine high resolution segmentation and hippocampal subfields segmentation?
Could someone please help?
Thanks.
Best regards, Hweeling
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.
oh, this may be a version mismatch then. Which version of FS are you using? On Tue, 21 Nov 2017, Hwee Ling Lee wrote:
Dear Bruce, Thanks for your reply. I checked the folder and did not find the file that was requested.
What I have in the average folder that has 'RB*.gca' are 'RB_all_2016-05-10.vc700.gca' and 'RB_all_withskull_2016-05-10.vc700.gca'. The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'.
Cheers, Hweeling
On Nov 21, 2017 18:05, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote: Hi Hweeling
what is FREESURFER_HOME set to in the environment? Does that file exist? It is a standard part of our distribution cheers Bruce On Tue, 21 Nov 2017, Hwee Ling Lee wrote: Dear all, I have T1 images collected from the 7T MRI scanner. I downloaded the most recent freesurfer software, and followed all instructions to install the software before using it. I would like to segment the T1 data using its high resolution image, and also to segment the hippocampal subfields. For command, I use this: recon-all -all -s <subject name> -hires -i <subject dicom T1 image frame 1 location> However, I get an error message: cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca I'm not sure what I did wrong. Also, how can I combine high resolution segmentation and hippocampal subfields segmentation? Could someone please help? Thanks. Best regards, Hweeling 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 Bruce,
I downloaded the latest version of freesurfer, "CentOS 6 x86_64 (64b)".
Cheers, Hweeling
On 21 November 2017 at 23:57, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
oh, this may be a version mismatch then. Which version of FS are you using?
On Tue, 21 Nov 2017, Hwee Ling Lee wrote:
Dear Bruce,
Thanks for your reply. I checked the folder and did not find the file that was requested.
What I have in the average folder that has 'RB*.gca' are 'RB_all_2016-05-10.vc700.gca' and 'RB_all_withskull_2016-05-10.vc700.gca'. The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'.
Cheers, Hweeling
On Nov 21, 2017 18:05, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote: Hi Hweeling
what is FREESURFER_HOME set to in the environment? Does that fileexist? It is a standard part of our distribution
cheers Bruce On Tue, 21 Nov 2017, Hwee Ling Lee wrote: Dear all, I have T1 images collected from the 7T MRI scanner. I downloaded the most recent freesurfer software, andfollowed all instructions to install the software before using it.
I would like to segment the T1 data using its high resolutionimage, and also to segment the hippocampal subfields.
For command, I use this: recon-all -all -s <subject name> -hires -i <subject dicom T1image frame 1 location>
However, I get an error message: cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca I'm not sure what I did wrong. Also, how can I combine high resolution segmentation andhippocampal subfields segmentation?
Could someone please help? Thanks. Best regards, Hweeling The information in this e-mail is intended only for the person towhom 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.
can you send us the recon-all.log? On Wed, 22 Nov 2017, Hwee Ling Lee wrote:
Hi Bruce,
I downloaded the latest version of freesurfer, "CentOS 6 x86_64 (64b)".
Cheers, Hweeling
On 21 November 2017 at 23:57, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: oh, this may be a version mismatch then. Which version of FS are you using? On Tue, 21 Nov 2017, Hwee Ling Lee wrote:
Dear Bruce, Thanks for your reply. I checked the folder and did not find the file that was requested. What I have in the average folder that has 'RB*.gca' are 'RB_all_2016-05-10.vc700.gca' and 'RB_all_withskull_2016-05-10.vc700.gca'. The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'. Cheers, Hweeling On Nov 21, 2017 18:05, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: Hi Hweeling what is FREESURFER_HOME set to in the environment? Does that file exist? It is a standard part of our distribution cheers Bruce On Tue, 21 Nov 2017, Hwee Ling Lee wrote: Dear all, I have T1 images collected from the 7T MRI scanner. I downloaded the most recent freesurfer software, and followed all instructions to install the software before using it. I would like to segment the T1 data using its high resolution image, and also to segment the hippocampal subfields. For command, I use this: recon-all -all -s <subject name> -hires -i <subject dicom T1 image frame 1 location> However, I get an error message: cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca I'm not sure what I did wrong. Also, how can I combine high resolution segmentation and hippocampal subfields segmentation? Could someone please help? Thanks. Best regards, Hweeling 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.
Dear Bruce,
Thanks for your patience. Attached you will find the screenshot of my server. In my institute's server, there is an older version of freesurfer, which I then change to a newer version before starting the recon-all.
I look forward to your reply.
Thanks.
Cheers, Hweeling
On 22 November 2017 at 15:31, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you send us the recon-all.log?
On Wed, 22 Nov 2017, Hwee Ling Lee wrote:
Hi Bruce,
I downloaded the latest version of freesurfer, "CentOS 6 x86_64 (64b)".
Cheers, Hweeling
On 21 November 2017 at 23:57, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: oh, this may be a version mismatch then. Which version of FS are you using? On Tue, 21 Nov 2017, Hwee Ling Lee wrote:
Dear Bruce, Thanks for your reply. I checked the folder and did not find the file that wasrequested.
What I have in the average folder that has 'RB*.gca' are 'RB_all_2016-05-10.vc700.gca' and 'RB_all_withskull_2016-05-10.vc700.gca'. The other file in that folder is'RB_all_2008-03-26.mni152.2mm.lta'.
Cheers, Hweeling On Nov 21, 2017 18:05, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: Hi Hweeling
what is FREESURFER_HOME set to in the environment? Doesthat file exist? It is a standard part of our distribution
cheers Bruce On Tue, 21 Nov 2017, Hwee Ling Lee wrote: Dear all, I have T1 images collected from the 7T MRIscanner.
I downloaded the most recent freesurfer software,and followed all instructions to install the software before using it.
I would like to segment the T1 data using itshigh resolution image, and also to segment the hippocampal subfields.
For command, I use this: recon-all -all -s <subject name> -hires -i<subject dicom T1 image frame 1 location>
However, I get an error message: cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca
I'm not sure what I did wrong. Also, how can I combine high resolutionsegmentation and hippocampal subfields segmentation?
Could someone please help? Thanks. Best regards, Hweeling The information in this e-mail is intended only for theperson 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 Hweeling
please don't send us screenshots of text - either attach the file or include text in the email.
I'm pretty sure you are using an older recon-all script with a newer FREESURFER_HOME. Try typing:
which recon-all
I bet it points to somewhere other than your V6 FREESURFER_HOME/bin dir
cheers Bruce
On Wed, 22 Nov 2017, Hwee Ling Lee wrote:
Dear Bruce,
Thanks for your patience. Attached you will find the screenshot of my server. In my institute's server, there is an older version of freesurfer, which I then change to a newer version before starting the recon-all.
I look forward to your reply.
Thanks.
Cheers, Hweeling
On 22 November 2017 at 15:31, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: can you send us the recon-all.log? On Wed, 22 Nov 2017, Hwee Ling Lee wrote:
Hi Bruce, I downloaded the latest version of freesurfer, "CentOS 6 x86_64 (64b)". Cheers, Hweeling On 21 November 2017 at 23:57, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: oh, this may be a version mismatch then. Which version of FS are you using? On Tue, 21 Nov 2017, Hwee Ling Lee wrote: Dear Bruce, Thanks for your reply. I checked the folder and did not find the file that was requested. What I have in the average folder that has 'RB*.gca' are 'RB_all_2016-05-10.vc700.gca' and 'RB_all_withskull_2016-05-10.vc700.gca'. The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'. Cheers, Hweeling On Nov 21, 2017 18:05, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: Hi Hweeling what is FREESURFER_HOME set to in the environment? Does that file exist? It is a standard part of our distribution cheers Bruce On Tue, 21 Nov 2017, Hwee Ling Lee wrote: Dear all, I have T1 images collected from the 7T MRI scanner. I downloaded the most recent freesurfer software, and followed all instructions to install the software before using it. I would like to segment the T1 data using its high resolution image, and also to segment the hippocampal subfields. For command, I use this: recon-all -all -s <subject name> -hires -i <subject dicom T1 image frame 1 location> However, I get an error message: cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca I'm not sure what I did wrong. Also, how can I combine high resolution segmentation and hippocampal subfields segmentation? Could someone please help? Thanks. Best regards, Hweeling 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.
Dear Bruce,
Sorry about the screenshot of text.
You are right that it still uses the older version of recon-all. How do I fix this then?
I can't delete the older version because I don't have access to it at all.
Thanks for your patience.
Cheers, Hweeling
On 22 November 2017 at 15:52, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Hweeling
please don't send us screenshots of text - either attach the file or include text in the email.
I'm pretty sure you are using an older recon-all script with a newer FREESURFER_HOME. Try typing:
which recon-all
I bet it points to somewhere other than your V6 FREESURFER_HOME/bin dir
cheers Bruce
On Wed, 22 Nov 2017, Hwee Ling Lee wrote:
Dear Bruce,
Thanks for your patience. Attached you will find the screenshot of my server. In my institute's server, there is an older version of freesurfer, which I then change to a newer version before starting the recon-all.
I look forward to your reply.
Thanks.
Cheers, Hweeling
On 22 November 2017 at 15:31, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: can you send us the recon-all.log? On Wed, 22 Nov 2017, Hwee Ling Lee wrote:
Hi Bruce, I downloaded the latest version of freesurfer, "CentOS 6x86_64 (64b)".
Cheers, Hweeling On 21 November 2017 at 23:57, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: oh, this may be a version mismatch then. Which version of FS are you using? On Tue, 21 Nov 2017, Hwee Ling Lee wrote:
Dear Bruce, Thanks for your reply. I checked the folder and did not find the filethat was requested.
What I have in the average folder that has'RB*.gca' are 'RB_all_2016-05-10.vc700.gca' and 'RB_all_withskull_2016-05-10.vc700.gca'. The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'.
Cheers, Hweeling On Nov 21, 2017 18:05, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: Hi Hweeling what is FREESURFER_HOME set to in theenvironment? Does that file exist? It is a standard part of our distribution
cheers Bruce On Tue, 21 Nov 2017, Hwee Ling Lee wrote: Dear all, I have T1 images collected from the7T MRI scanner.
I downloaded the most recentfreesurfer software, and followed all instructions to install the software before using it.
I would like to segment the T1 datausing its high resolution image, and also to segment the hippocampal subfields.
For command, I use this: recon-all -all -s <subject name>-hires -i <subject dicom T1 image frame 1 location>
However, I get an error message: cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca I'm not sure what I did wrong. Also, how can I combine highresolution segmentation and hippocampal subfields segmentation?
Could someone please help? Thanks. Best regards, Hweeling The information in this e-mail is intendedonly for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
you need to change your path so that
which recon-all
gives you the v6 one. something like:
set path = ($FREESURFER_HOME/bin $path) rehash
where FREESURFER_HOME points to the v6 version cheers Bruce
On Wed, 22 Nov 2017, Hwee Ling Lee wrote:
Dear Bruce,
Sorry about the screenshot of text.
You are right that it still uses the older version of recon-all. How do I fix this then?
I can't delete the older version because I don't have access to it at all.
Thanks for your patience.
Cheers, Hweeling
On 22 November 2017 at 15:52, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Hweeling
please don't send us screenshots of text - either attach the file or include text in the email. I'm pretty sure you are using an older recon-all script with a newer FREESURFER_HOME. Try typing: which recon-all I bet it points to somewhere other than your V6 FREESURFER_HOME/bin dir cheers Bruce On Wed, 22 Nov 2017, Hwee Ling Lee wrote: Dear Bruce, Thanks for your patience. Attached you will find the screenshot of my server. In my institute's server, there is an older version of freesurfer, which I then change to a newer version before starting the recon-all. I look forward to your reply. Thanks. Cheers, Hweeling On 22 November 2017 at 15:31, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: can you send us the recon-all.log? On Wed, 22 Nov 2017, Hwee Ling Lee wrote: Hi Bruce, I downloaded the latest version of freesurfer, "CentOS 6 x86_64 (64b)". Cheers, Hweeling On 21 November 2017 at 23:57, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: oh, this may be a version mismatch then. Which version of FS are you using? On Tue, 21 Nov 2017, Hwee Ling Lee wrote: Dear Bruce, Thanks for your reply. I checked the folder and did not find the file that was requested. What I have in the average folder that has 'RB*.gca' are 'RB_all_2016-05-10.vc700.gca' and 'RB_all_withskull_2016-05-10.vc700.gca'. The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'. Cheers, Hweeling On Nov 21, 2017 18:05, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: Hi Hweeling what is FREESURFER_HOME set to in the environment? Does that file exist? It is a standard part of our distribution cheers Bruce On Tue, 21 Nov 2017, Hwee Ling Lee wrote: Dear all, I have T1 images collected from the 7T MRI scanner. I downloaded the most recent freesurfer software, and followed all instructions to install the software before using it. I would like to segment the T1 data using its high resolution image, and also to segment the hippocampal subfields. For command, I use this: recon-all -all -s <subject name> -hires -i <subject dicom T1 image frame 1 location> However, I get an error message: cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca I'm not sure what I did wrong. Also, how can I combine high resolution segmentation and hippocampal subfields segmentation? Could someone please help? Thanks. Best regards, Hweeling 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.
Dear Bruce,
Thanks for your tip. Actually, it didn't work for me. I went to ask one of my colleagues, Martin Reuter, for help, and it turns out that the permission of my files in the $FREESURFER_HOME/bin folder have been changed to 'read only'. Martin helped me to change the files in the $FREESURFER_HOME/bin folder to all executable files by using this command: 'chmod u+w *'.
Hence, I'm replying to this thread so that I hope this will help others in the future with similar problems.
Thanks again for your patience!
Cheers, Hweeling
On 23 November 2017 at 16:24, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
you need to change your path so that
which recon-all
gives you the v6 one. something like:
set path = ($FREESURFER_HOME/bin $path) rehash
where FREESURFER_HOME points to the v6 version
cheers Bruce
On Wed, 22 Nov 2017, Hwee Ling Lee wrote:
Dear Bruce,
Sorry about the screenshot of text.
You are right that it still uses the older version of recon-all. How do I fix this then?
I can't delete the older version because I don't have access to it at all.
Thanks for your patience.
Cheers, Hweeling
On 22 November 2017 at 15:52, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Hweeling
please don't send us screenshots of text - either attach the file or include text in the email. I'm pretty sure you are using an older recon-all script with a newer FREESURFER_HOME. Try typing: which recon-all I bet it points to somewhere other than your V6 FREESURFER_HOME/bin dir cheers Bruce On Wed, 22 Nov 2017, Hwee Ling Lee wrote: Dear Bruce, Thanks for your patience. Attached you will find the screenshot of my server. In my institute's server, there is an older version of freesurfer, which I then change to a newer version before starting the recon-all. I look forward to your reply. Thanks. Cheers, Hweeling On 22 November 2017 at 15:31, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: can you send us the recon-all.log? On Wed, 22 Nov 2017, Hwee Ling Lee wrote: Hi Bruce, I downloaded the latest version of freesurfer, "CentOS 6 x86_64 (64b)". Cheers, Hweeling On 21 November 2017 at 23:57, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: oh, this may be a version mismatch then. Which version of FS are you using? On Tue, 21 Nov 2017, Hwee Ling Lee wrote: Dear Bruce, Thanks for your reply. I checked the folder and did not find the file that was requested. What I have in the average folder that has 'RB*.gca' are 'RB_all_2016-05-10.vc700.gca' and 'RB_all_withskull_2016-05-10.vc700.gca'. The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'. Cheers, Hweeling On Nov 21, 2017 18:05, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: Hi Hweeling what is FREESURFER_HOME set to in the environment? Does that file exist? It is a standard part of our distribution cheers Bruce On Tue, 21 Nov 2017, Hwee Ling Lee wrote: Dear all, I have T1 images collected from the 7T MRI scanner. I downloaded the most recent freesurfer software, and followed all instructions to install the software before using it. I would like to segment the T1 data using its high resolution image, and also to segment the hippocampal subfields. For command, I use this: recon-all -all -s <subject name> -hires -i <subject dicom T1 image frame 1 location> However, I get an error message: cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca I'm not sure what I did wrong. Also, how can I combine high resolution segmentation and hippocampal subfields segmentation? Could someone please help? Thanks. Best regards, Hweeling 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.
I'm glad to hear it worked out Bruce On Tue, 28 Nov 2017, Hwee Ling Lee wrote:
Dear Bruce, Thanks for your tip. Actually, it didn't work for me. I went to ask one of my colleagues, Martin Reuter, for help, and it turns out that the permission of my files in the $FREESURFER_HOME/bin folder have been changed to 'read only'. Martin helped me to change the files in the $FREESURFER_HOME/bin folder to all executable files by using this command: 'chmod u+w *'.
Hence, I'm replying to this thread so that I hope this will help others in the future with similar problems.
Thanks again for your patience!
Cheers, Hweeling
On 23 November 2017 at 16:24, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: you need to change your path so that
which recon-all gives you the v6 one. something like: set path = ($FREESURFER_HOME/bin $path) rehash where FREESURFER_HOME points to the v6 version cheers Bruce On Wed, 22 Nov 2017, Hwee Ling Lee wrote: Dear Bruce, Sorry about the screenshot of text. You are right that it still uses the older version of recon-all. How do I fix this then? I can't delete the older version because I don't have access to it at all. Thanks for your patience. Cheers, Hweeling On 22 November 2017 at 15:52, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Hweeling please don't send us screenshots of text - either attach the file or include text in the email. I'm pretty sure you are using an older recon-all script with a newer FREESURFER_HOME. Try typing: which recon-all I bet it points to somewhere other than your V6 FREESURFER_HOME/bin dir cheers Bruce On Wed, 22 Nov 2017, Hwee Ling Lee wrote: Dear Bruce, Thanks for your patience. Attached you will find the screenshot of my server. In my institute's server, there is an older version of freesurfer, which I then change to a newer version before starting the recon-all. I look forward to your reply. Thanks. Cheers, Hweeling On 22 November 2017 at 15:31, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: can you send us the recon-all.log? On Wed, 22 Nov 2017, Hwee Ling Lee wrote: Hi Bruce, I downloaded the latest version of freesurfer, "CentOS 6 x86_64 (64b)". Cheers, Hweeling On 21 November 2017 at 23:57, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: oh, this may be a version mismatch then. Which version of FS are you using? On Tue, 21 Nov 2017, Hwee Ling Lee wrote: Dear Bruce, Thanks for your reply. I checked the folder and did not find the file that was requested. What I have in the average folder that has 'RB*.gca' are 'RB_all_2016-05-10.vc700.gca' and 'RB_all_withskull_2016-05-10.vc700.gca'. The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'. Cheers, Hweeling On Nov 21, 2017 18:05, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: Hi Hweeling what is FREESURFER_HOME set to in the environment? Does that file exist? It is a standard part of our distribution cheers Bruce On Tue, 21 Nov 2017, Hwee Ling Lee wrote: Dear all, I have T1 images collected from the 7T MRI scanner. I downloaded the most recent freesurfer software, and followed all instructions to install the software before using it. I would like to segment the T1 data using its high resolution image, and also to segment the hippocampal subfields. For command, I use this: recon-all -all -s <subject name> -hires -i <subject dicom T1 image frame 1 location> However, I get an error message: cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca I'm not sure what I did wrong. Also, how can I combine high resolution segmentation and hippocampal subfields segmentation? Could someone please help? Thanks. Best regards, Hweeling The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Dear FS developers,
I have problem as follow when I tried file input/output (original images can not be identified)
Xues-MacBook-Air:00000001 DannyDeng$ recon-all -i im_0001.dcm ERROR: must specify a subject id Xues-MacBook-Air:00000001 DannyDeng$ recon-all -i IM_0001.dcm -s anon mkdir: /Applications/freesurfer/subjects/anon: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied cp: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory cat: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c /Applications/freesurfer/subjects/anon/scripts/patchdir.txt: No such file or directory. Xues-MacBook-Air:00000001 DannyDeng$ recon-all -i IM_0001.dcm -s anon mkdir: /Applications/freesurfer/subjects/anon: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied cp: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory cat: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c /Applications/freesurfer/subjects/anon/scripts/patchdir.txt: No such file or directory. Xues-MacBook-Air:00000001 DannyDeng$
Please help.
Thanks.
Best Regards, Danny Deng
On Nov 22, 2017, at 1:33 AM, Hwee Ling Lee hweeling.lee@gmail.com wrote:
Dear Bruce,
Thanks for your reply. I checked the folder and did not find the file that was requested.
What I have in the average folder that has 'RB*.gca' are 'RB_all_2016-05-10.vc700.gca' and 'RB_all_withskull_2016-05-10.vc700.gca'. The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'.
Cheers, Hweeling
On Nov 21, 2017 18:05, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote: Hi Hweeling
what is FREESURFER_HOME set to in the environment? Does that file exist? It is a standard part of our distribution
cheers Bruce
On Tue, 21 Nov 2017, Hwee Ling Lee wrote:
Dear all,
I have T1 images collected from the 7T MRI scanner.
I downloaded the most recent freesurfer software, and followed all instructions to install the software before using it.
I would like to segment the T1 data using its high resolution image, and also to segment the hippocampal subfields.
For command, I use this:
recon-all -all -s <subject name> -hires -i <subject dicom T1 image frame 1 location>
However, I get an error message:
cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca
I'm not sure what I did wrong.
Also, how can I combine high resolution segmentation and hippocampal subfields segmentation?
Could someone please help?
Thanks.
Best regards, Hweeling
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Danny
you need to specify a subject name/id with -s <id>
cheers Bruce On Wed, 22 Nov 2017, Danny Deng wrote:
Dear FS developers, I have problem as follow when I tried file input/output (original images can not be identified)
Xues-MacBook-Air:00000001 DannyDeng$ recon-all -i im_0001.dcm ERROR: must specify a subject id Xues-MacBook-Air:00000001 DannyDeng$ recon-all -i IM_0001.dcm -s anon mkdir: /Applications/freesurfer/subjects/anon: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied cp: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory cat: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c /Applications/freesurfer/subjects/anon/scripts/patchdir.txt: No such file or directory. Xues-MacBook-Air:00000001 DannyDeng$ recon-all -i IM_0001.dcm -s anon mkdir: /Applications/freesurfer/subjects/anon: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied cp: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory cat: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c /Applications/freesurfer/subjects/anon/scripts/patchdir.txt: No such file or directory. Xues-MacBook-Air:00000001 DannyDeng$
Please help.
Thanks.
Best Regards,Danny Deng
On Nov 22, 2017, at 1:33 AM, Hwee Ling Lee <hweeling.lee@gmail.com> wrote:Dear Bruce, Thanks for your reply. I checked the folder and did not find the file that was requested.
What I have in the average folder that has 'RB*.gca' are 'RB_all_2016-05-10.vc700.gca' and 'RB_all_withskull_2016-05-10.vc700.gca'. The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'.
Cheers, Hweeling
On Nov 21, 2017 18:05, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote: Hi Hweeling
what is FREESURFER_HOME set to in the environment? Does that file exist? It is a standard part of our distribution cheers Bruce On Tue, 21 Nov 2017, Hwee Ling Lee wrote: Dear all, I have T1 images collected from the 7T MRI scanner. I downloaded the most recent freesurfer software, and followed all instructions to install the software before using it. I would like to segment the T1 data using its high resolution image, and also to segment the hippocampal subfields. For command, I use this: recon-all -all -s <subject name> -hires -i <subject dicom T1 image frame 1 location> However, I get an error message: cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca I'm not sure what I did wrong. Also, how can I combine high resolution segmentation and hippocampal subfields segmentation? Could someone please help? Thanks. Best regards, Hweeling 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.
freesurfer@nmr.mgh.harvard.edu
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Danny Deng -
Hwee Ling Lee