Hi Zeke,
We tried the new version of mri_cc and we still do not get 12 segments of the corpus callosum when we open the aseg.12segmentsCC.mgz in a viewer.
Could you send us the script you launch after the recon_all to get aseg.mgz files with 12 segments? basically the mri_cc
Could you also please explain how to edit the ColorLut.txt file
Finally, what is the precise script of the mri_segstats to generate stats tables.
Thanks again,
Cheers, Genevieve
On Tue, Nov 24, 2015 at 11:20 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
Hello Genevieve,
Below is a link to the newest version of mri_cc. Please copy it to your FREESURFER_HOME directory and backup the original.
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_cc
Hope this help.
-Zeke
On 11/24/2015 05:56 AM, UQAM wrote:
Hi Bruce,
DELL R910 Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 cores) 32 Go RAM CentOS release 5.10 (Final) kernel 2.6.18-371.3.1.el5
On Mon, Nov 23, 2015 at 7:32 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Genevieve I just tracked this down and it is a bug in mri_cc. If you tell Zeke your hardware/software environment he can get you a new version that should work cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi Bruce, Please find the two files attached. Genevieve On Mon, Nov 23, 2015 at 2:39 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Geneviève if you send us the $SUBJECTS_DIR/CColorLUT.txt and $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a look cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi, This a a "re-posting" of a question I've raised last week ; ) I would like to segment the corpus callosum into twelve even lenght segments instead of the five segments that freesurfer includes by default. - First I ran a mri_cc on subject e0070: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC.mgz -d 12 e0070 - Then I edited the ColorLUT.txt file and renamed it CColorLUT.txt (see attachment, segments 251 to 262). - Finally I ran a mri_segstats to compute the statistics on segmented volumes. mri_segstats seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 sum --e0070_CC12.aseg.stats The e0070_CC12.aseg.stats file still displays only five segments of the corpus callosum. Any tips or clues on how I could do things differently to get 12 segments? Thanks in advance, Geneviève _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.eduhttps://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
Hi Genevieve
are you sure you are using the correct mri_cc? I used your command line and got 12 segments. How many segents do you get? It should generate segments numbered 230-241 I think. You'll need to make your own entries in the ColorLUT.txt file if you want to see them in prespecified colors and names and such
cheers Bruce On Fri, 27 Nov 2015, UQAM wrote:
Hi Zeke, We tried the new version of mri_cc and we still do not get 12 segments of the corpus callosum when we open the aseg.12segmentsCC.mgz in a viewer.
Could you send us the script you launch after the recon_all to get aseg.mgz files with 12 segments? basically the mri_cc
Could you also please explain how to edit the ColorLut.txt file
Finally, what is the precise script of the mri_segstats to generate stats tables.
Thanks again,
Cheers, Genevieve
On Tue, Nov 24, 2015 at 11:20 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote: Hello Genevieve,
Below is a link to the newest version of mri_cc. Please copy it to your FREESURFER_HOME directory and backup the original. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_cc Hope this help. -Zeke On 11/24/2015 05:56 AM, UQAM wrote: Hi Bruce, DELL R910 Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 cores) 32 Go RAM CentOS release 5.10 (Final) kernel 2.6.18-371.3.1.el5 On Mon, Nov 23, 2015 at 7:32 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Genevieve I just tracked this down and it is a bug in mri_cc. If you tell Zeke your hardware/software environment he can get you a new version that should work cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi Bruce, Please find the two files attached. Genevieve On Mon, Nov 23, 2015 at 2:39 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Geneviève if you send us the $SUBJECTS_DIR/CColorLUT.txt and $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a look cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi, This a a "re-posting" of a question I've raised last week ; ) I would like to segment the corpus callosum into twelve even lenght segments instead of the five segments that freesurfer includes by default. - First I ran a mri_cc on subject e0070: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC.mgz -d 12 e0070 - Then I edited the ColorLUT.txt file and renamed it CColorLUT.txt (see attachment, segments 251 to 262). - Finally I ran a mri_segstats to compute the statistics on segmented volumes. mri_segstats seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 sum --e0070_CC12.aseg.stats The e0070_CC12.aseg.stats file still displays only five segments of the corpus callosum. Any tips or clues on how I could do things differently to get 12 segments? Thanks in advance, Geneviève _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 mailto: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
Hi Bruce,
We were using the correct mri_cc, but our segments were numbered 251 to 262 instead of 230 to 241 in the CColorLUT.txt. With this adjustment, the mri_cc now runs perfectly and segments in 12.
Many thanks for your support!
Best, Genevieve
On Fri, Nov 27, 2015 at 3:58 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Genevieve
are you sure you are using the correct mri_cc? I used your command line and got 12 segments. How many segents do you get? It should generate segments numbered 230-241 I think. You'll need to make your own entries in the ColorLUT.txt file if you want to see them in prespecified colors and names and such
cheers Bruce
On Fri, 27 Nov 2015, UQAM wrote:
Hi Zeke,
We tried the new version of mri_cc and we still do not get 12 segments of the corpus callosum when we open the aseg.12segmentsCC.mgz in a viewer.
Could you send us the script you launch after the recon_all to get aseg.mgz files with 12 segments? basically the mri_cc
Could you also please explain how to edit the ColorLut.txt file
Finally, what is the precise script of the mri_segstats to generate stats tables.
Thanks again,
Cheers, Genevieve
On Tue, Nov 24, 2015 at 11:20 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote: Hello Genevieve,
Below is a link to the newest version of mri_cc. Please copy it toyour FREESURFER_HOME directory and backup the original.
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_cc
Hope this help. -Zeke On 11/24/2015 05:56 AM, UQAM wrote: Hi Bruce, DELL R910 Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 cores) 32 Go RAM CentOS release 5.10 (Final) kernel 2.6.18-371.3.1.el5 On Mon, Nov 23, 2015 at 7:32 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote:
Hi Genevieve I just tracked this down and it is a bug in mri_cc. Ifyou tell Zeke your hardware/software environment he can get you a new version that should work
cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi Bruce, Please find the two files attached. Genevieve On Mon, Nov 23, 2015 at 2:39 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Geneviève
if you send us the $SUBJECTS_DIR/CColorLUT.txtand $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a look
cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi, This a a "re-posting" of a question I'veraised last week ; )
I would like to segment the corpuscallosum into twelve even lenght segments instead of the five segments that freesurfer includes by default.
- First I ran a mri_cc on subject e0070: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC.mgz -d 12 e0070 - Then I edited the ColorLUT.txt fileand renamed it CColorLUT.txt (see attachment, segments 251 to 262).
- Finally I ran a mri_segstats tocompute the statistics on segmented volumes.
mri_segstats seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty--excludeid 0 sum --e0070_CC12.aseg.stats
The e0070_CC12.aseg.stats file stilldisplays only five segments of the corpus callosum.
Any tips or clues on how I could dothings differently to get 12 segments?
Thanks in advance, Geneviève _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.eduhttps://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
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 Genevieve
I just reran it locally and confirmed that the segments start at 230 for me, so I'm not sure what's going on. Still, maybe it meets your needs for now (but be aware that when we release V6 the segment numbering is likely to start at 230)
cheers Bruce
On Fri, 4 Dec 2015, UQAM wrote:
Hi Bruce, We were using the correct mri_cc, but our segments were numbered 251 to 262 instead of 230 to 241 in the CColorLUT.txt. With this adjustment, the mri_cc now runs perfectly and segments in 12.
Many thanks for your support!
Best, Genevieve
On Fri, Nov 27, 2015 at 3:58 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Genevieve
are you sure you are using the correct mri_cc? I used your command line and got 12 segments. How many segents do you get? It should generate segments numbered 230-241 I think. You'll need to make your own entries in the ColorLUT.txt file if you want to see them in prespecified colors and names and such cheers Bruce On Fri, 27 Nov 2015, UQAM wrote: Hi Zeke, We tried the new version of mri_cc and we still do not get 12 segments of the corpus callosum when we open the aseg.12segmentsCC.mgz in a viewer. Could you send us the script you launch after the recon_all to get aseg.mgz files with 12 segments? basically the mri_cc Could you also please explain how to edit the ColorLut.txt file Finally, what is the precise script of the mri_segstats to generate stats tables. Thanks again, Cheers, Genevieve On Tue, Nov 24, 2015 at 11:20 PM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote: Hello Genevieve, Below is a link to the newest version of mri_cc. Please copy it to your FREESURFER_HOME directory and backup the original. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_cc Hope this help. -Zeke On 11/24/2015 05:56 AM, UQAM wrote: Hi Bruce, DELL R910 Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 cores) 32 Go RAM CentOS release 5.10 (Final) kernel 2.6.18-371.3.1.el5 On Mon, Nov 23, 2015 at 7:32 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Genevieve I just tracked this down and it is a bug in mri_cc. If you tell Zeke your hardware/software environment he can get you a new version that should work cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi Bruce, Please find the two files attached. Genevieve On Mon, Nov 23, 2015 at 2:39 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Geneviève if you send us the $SUBJECTS_DIR/CColorLUT.txt and $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a look cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi, This a a "re-posting" of a question I've raised last week ; ) I would like to segment the corpus callosum into twelve even lenght segments instead of the five segments that freesurfer includes by default. - First I ran a mri_cc on subject e0070: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC.mgz -d 12 e0070 - Then I edited the ColorLUT.txt file and renamed it CColorLUT.txt (see attachment, segments 251 to 262). - Finally I ran a mri_segstats to compute the statistics on segmented volumes. mri_segstats seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 sum --e0070_CC12.aseg.stats The e0070_CC12.aseg.stats file still displays only five segments of the corpus callosum. Any tips or clues on how I could do things differently to get 12 segments? Thanks in advance, Geneviève _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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
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 again Bruce,
The mri_cc & mri_segstats run just fine. - When I open the open the new segmented .mgz files (aseg.12segmentsCC_new.mgz) in tkmedit I can clearly visualize the 12 segments. - When I open the .stats file I get volumes for each of the 12 corpus callosum segments.
However, when I run the asegstats2table the result is a .txt file with the usual 5 segments of the corpus callosum (anterior, ...).
Any clue why the asegstats2table doesn't take into account the new 12 segments?
See relevant files attached,
As usual thanks so much ; ) Genevieve
On Fri, Dec 4, 2015 at 3:07 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Genevieve
I just reran it locally and confirmed that the segments start at 230 for me, so I'm not sure what's going on. Still, maybe it meets your needs for now (but be aware that when we release V6 the segment numbering is likely to start at 230)
cheers Bruce
On Fri, 4 Dec 2015, UQAM wrote:
Hi Bruce,
We were using the correct mri_cc, but our segments were numbered 251 to 262 instead of 230 to 241 in the CColorLUT.txt. With this adjustment, the mri_cc now runs perfectly and segments in 12.
Many thanks for your support!
Best, Genevieve
On Fri, Nov 27, 2015 at 3:58 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Genevieve
are you sure you are using the correct mri_cc? I used your commandline and got 12 segments. How many segents do you get? It should generate segments numbered 230-241 I think. You'll need to make your own entries in the ColorLUT.txt file if you want to see them in prespecified colors and names and such
cheers Bruce On Fri, 27 Nov 2015, UQAM wrote: Hi Zeke, We tried the new version of mri_cc and we still do not get 12segments of the corpus callosum when we open the aseg.12segmentsCC.mgz in a viewer.
Could you send us the script you launch after the recon_allto get aseg.mgz files with 12 segments? basically the mri_cc
Could you also please explain how to edit the ColorLut.txtfile
Finally, what is the precise script of the mri_segstats togenerate stats tables.
Thanks again, Cheers, Genevieve On Tue, Nov 24, 2015 at 11:20 PM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote: Hello Genevieve,
Below is a link to the newest version of mri_cc. Pleasecopy it to your FREESURFER_HOME directory and backup the original.
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_cc
Hope this help. -Zeke On 11/24/2015 05:56 AM, UQAM wrote: Hi Bruce, DELL R910 Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 cores) 32 Go RAM CentOS release 5.10 (Final) kernel 2.6.18-371.3.1.el5 On Mon, Nov 23, 2015 at 7:32 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Genevieve I just tracked this down and it is a bug inmri_cc. If you tell Zeke your hardware/software environment he can get you a new version that should work
cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi Bruce, Please find the two files attached. Genevieve On Mon, Nov 23, 2015 at 2:39 PM, BruceFischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote: Hi Geneviève
if you send us the$SUBJECTS_DIR/CColorLUT.txt and
$SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a look
cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi, This a a "re-posting" of aquestion I've raised last week ; )
I would like to segment thecorpus callosum into twelve even lenght segments instead of the five segments that freesurfer includes by default.
- First I ran a mri_cc onsubject e0070:
mri_cc -asegaseg.auto_noCCseg.mgz -o aseg.12segmentsCC.mgz -d 12 e0070
- Then I edited theColorLUT.txt file and renamed it CColorLUT.txt (see attachment, segments 251 to 262).
- Finally I ran amri_segstats to compute the statistics on segmented volumes.
mri_segstats seg$SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 sum --e0070_CC12.aseg.stats
The e0070_CC12.aseg.statsfile still displays only five segments of the corpus callosum.
Any tips or clues on how Icould do things differently to get 12 segments?
Thanks in advance, Geneviève
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only forthe 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 <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
_______________________________________________ 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.
HI Genevieve
you'll need to send us all your command lines
cheers Bruce
On Fri, 4 Dec 2015, UQAM wrote:
Hi again Bruce, The mri_cc & mri_segstats run just fine.
- When I open the open the new segmented .mgz files (aseg.12segmentsCC_new.mgz) in tkmedit I can
clearly visualize the 12 segments.
- When I open the .stats file I get volumes for each of the 12 corpus callosum segments.
However, when I run the asegstats2table the result is a .txt file with the usual 5 segments of the corpus callosum (anterior, ...).
Any clue why the asegstats2table doesn't take into account the new 12 segments?
See relevant files attached,
As usual thanks so much ; ) Genevieve
On Fri, Dec 4, 2015 at 3:07 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Genevieve
I just reran it locally and confirmed that the segments start at 230 for me, so I'm not sure what's going on. Still, maybe it meets your needs for now (but be aware that when we release V6 the segment numbering is likely to start at 230) cheers Bruce On Fri, 4 Dec 2015, UQAM wrote: Hi Bruce, We were using the correct mri_cc, but our segments were numbered 251 to 262 instead of 230 to 241 in the CColorLUT.txt. With this adjustment, the mri_cc now runs perfectly and segments in 12. Many thanks for your support! Best, Genevieve On Fri, Nov 27, 2015 at 3:58 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Genevieve are you sure you are using the correct mri_cc? I used your command line and got 12 segments. How many segents do you get? It should generate segments numbered 230-241 I think. You'll need to make your own entries in the ColorLUT.txt file if you want to see them in prespecified colors and names and such cheers Bruce On Fri, 27 Nov 2015, UQAM wrote: Hi Zeke, We tried the new version of mri_cc and we still do not get 12 segments of the corpus callosum when we open the aseg.12segmentsCC.mgz in a viewer. Could you send us the script you launch after the recon_all to get aseg.mgz files with 12 segments? basically the mri_cc Could you also please explain how to edit the ColorLut.txt file Finally, what is the precise script of the mri_segstats to generate stats tables. Thanks again, Cheers, Genevieve On Tue, Nov 24, 2015 at 11:20 PM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote: Hello Genevieve, Below is a link to the newest version of mri_cc. Please copy it to your FREESURFER_HOME directory and backup the original. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_cc Hope this help. -Zeke On 11/24/2015 05:56 AM, UQAM wrote: Hi Bruce, DELL R910 Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 cores) 32 Go RAM CentOS release 5.10 (Final) kernel 2.6.18-371.3.1.el5 On Mon, Nov 23, 2015 at 7:32 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Genevieve I just tracked this down and it is a bug in mri_cc. If you tell Zeke your hardware/software environment he can get you a new version that should work cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi Bruce, Please find the two files attached. Genevieve On Mon, Nov 23, 2015 at 2:39 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Geneviève if you send us the $SUBJECTS_DIR/CColorLUT.txt and $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a look cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi, This a a "re-posting" of a question I've raised last week ; ) I would like to segment the corpus callosum into twelve even lenght segments instead of the five segments that freesurfer includes by default. - First I ran a mri_cc on subject e0070: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC.mgz -d 12 e0070 - Then I edited the ColorLUT.txt file and renamed it CColorLUT.txt (see attachment, segments 251 to 262). - Finally I ran a mri_segstats to compute the statistics on segmented volumes. mri_segstats seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 sum --e0070_CC12.aseg.stats The e0070_CC12.aseg.stats file still displays only five segments of the corpus callosum. Any tips or clues on how I could do things differently to get 12 segments? Thanks in advance, Geneviève _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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 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,
We used these:
mri_cc_new -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC_new.mgz -d 12 e0070 ... (for all the subjects from e0042 to a0040)
mri_segstats --seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC_new.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 --sum $SUBJECTS_DIR/e0070/stats/e0070_CC12_new.aseg.stats .... (for all the subjects from e0042 to a0040)
asegstats2table --subjects e0042 e0041 e0035 e0048 e0058 e0059 e0053 e0032 e0047 e0036 e0039 e0049 e0051 e0050 e0045 e0061 e0062 e0063 e0064 e0065 e0066 e0067 e0068 e0070 e0071 e0072 e0073 e0074 e0075 e0076 e0077 e0021 e0004 e0078 e0079 e0080 e0013 e0081 e0082 e0083 a0001 a0002 a0003 a0004 a0005 a0006 a0007 a0008 a0009 a0010 a0011 a0012 a0013 a0014 a0015 a0016 a0017 a0018 a0019 a0020 a0021 a0022 a0023 a0024 a0025 a0026 a0027 a0028 a0029 a0030 a0031 a0032 a0033 a0034 a0035 a0036 a0037 a0038 a0039 a0040 --meas volume --tablefile aseg_stats_12CC_new.txt
Genevieve
On Fri, Dec 4, 2015 at 5:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
HI Genevieve
you'll need to send us all your command lines
cheers Bruce
On Fri, 4 Dec 2015, UQAM wrote:
Hi again Bruce,
The mri_cc & mri_segstats run just fine.
- When I open the open the new segmented .mgz files
(aseg.12segmentsCC_new.mgz) in tkmedit I can clearly visualize the 12 segments.
- When I open the .stats file I get volumes for each of the 12 corpus
callosum segments.
However, when I run the asegstats2table the result is a .txt file with the usual 5 segments of the corpus callosum (anterior, ...).
Any clue why the asegstats2table doesn't take into account the new 12 segments?
See relevant files attached,
As usual thanks so much ; ) Genevieve
On Fri, Dec 4, 2015 at 3:07 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Genevieve
I just reran it locally and confirmed that the segments start at230 for me, so I'm not sure what's going on. Still, maybe it meets your needs for now (but be aware that when we release V6 the segment numbering is likely to start at 230)
cheers Bruce On Fri, 4 Dec 2015, UQAM wrote: Hi Bruce, We were using the correct mri_cc, but our segments werenumbered 251 to 262 instead of 230 to 241 in the CColorLUT.txt. With this adjustment, the mri_cc now runs perfectly and segments in 12.
Many thanks for your support! Best, Genevieve On Fri, Nov 27, 2015 at 3:58 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Genevieve
are you sure you are using the correct mri_cc? I usedyour command line and got 12 segments. How many segents do you get? It should generate segments numbered 230-241 I think. You'll need to make your own entries in the ColorLUT.txt file if you want to see them in prespecified colors and names and such
cheers Bruce On Fri, 27 Nov 2015, UQAM wrote: Hi Zeke, We tried the new version of mri_cc and we stilldo not get 12 segments of the corpus callosum when we open the aseg.12segmentsCC.mgz in a viewer.
Could you send us the script you launch after therecon_all to get aseg.mgz files with 12 segments? basically the mri_cc
Could you also please explain how to edit theColorLut.txt file
Finally, what is the precise script of themri_segstats to generate stats tables.
Thanks again, Cheers, Genevieve On Tue, Nov 24, 2015 at 11:20 PM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote: Hello Genevieve, Below is a link to the newest version ofmri_cc. Please copy it to your FREESURFER_HOME directory and backup the original.
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_cc
Hope this help. -Zeke On 11/24/2015 05:56 AM, UQAM wrote: Hi Bruce, DELL R910 Intel(R) Xeon(R) CPU E7520 @ 1.87GHz(16 cores) 32 Go RAM CentOS release 5.10 (Final) kernel 2.6.18-371.3.1.el5
On Mon, Nov 23, 2015 at 7:32 PM,Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Genevieve I just tracked this down and itis a bug in mri_cc. If you tell Zeke your hardware/software environment he can get you a new version that should work
cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi Bruce, Please find the two filesattached.
Genevieve On Mon, Nov 23, 2015 at 2:39PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote: Hi Geneviève
if you send us the $SUBJECTS_DIR/CColorLUT.txt and $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a look cheers Bruce On Mon, 23 Nov 2015,UQAM wrote:
Hi, This a a"re-posting" of a question I've raised last week ; )
I would like tosegment the corpus callosum into twelve even lenght segments instead of the five segments that freesurfer includes by default.
- First I ran amri_cc on subject e0070:
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC.mgz -d 12e0070
- Then I editedthe ColorLUT.txt file and renamed it CColorLUT.txt (see attachment, segments 251 to 262).
- Finally I rana mri_segstats to compute the statistics on segmented volumes.
mri_segstats seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab$SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 sum
--e0070_CC12.aseg.stats
Thee0070_CC12.aseg.stats file still displays only five segments of the corpus callosum.
Any tips orclues on how I could do things differently to get 12 segments?
Thanks inadvance,
Geneviève _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail isintended 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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 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.
Can you send me one of the e0070_CC12_new.aseg.stats files?
On 12/06/2015 08:12 AM, UQAM wrote:
Hi Bruce,
We used these:
mri_cc_new -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC_new.mgz -d 12 e0070 ... (for all the subjects from e0042 to a0040)
mri_segstats --seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC_new.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 --sum $SUBJECTS_DIR/e0070/stats/e0070_CC12_new.aseg.stats .... (for all the subjects from e0042 to a0040)
asegstats2table --subjects e0042 e0041 e0035 e0048 e0058 e0059 e0053 e0032 e0047 e0036 e0039 e0049 e0051 e0050 e0045 e0061 e0062 e0063 e0064 e0065 e0066 e0067 e0068 e0070 e0071 e0072 e0073 e0074 e0075 e0076 e0077 e0021 e0004 e0078 e0079 e0080 e0013 e0081 e0082 e0083 a0001 a0002 a0003 a0004 a0005 a0006 a0007 a0008 a0009 a0010 a0011 a0012 a0013 a0014 a0015 a0016 a0017 a0018 a0019 a0020 a0021 a0022 a0023 a0024 a0025 a0026 a0027 a0028 a0029 a0030 a0031 a0032 a0033 a0034 a0035 a0036 a0037 a0038 a0039 a0040 --meas volume --tablefile aseg_stats_12CC_new.txt
Genevieve
On Fri, Dec 4, 2015 at 5:56 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
HI Genevieve you'll need to send us all your command lines cheers Bruce On Fri, 4 Dec 2015, UQAM wrote: Hi again Bruce, The mri_cc & mri_segstats run just fine. - When I open the open the new segmented .mgz files (aseg.12segmentsCC_new.mgz) in tkmedit I can clearly visualize the 12 segments. - When I open the .stats file I get volumes for each of the 12 corpus callosum segments. However, when I run the asegstats2table the result is a .txt file with the usual 5 segments of the corpus callosum (anterior, ...). Any clue why the asegstats2table doesn't take into account the new 12 segments? See relevant files attached, As usual thanks so much ; ) Genevieve On Fri, Dec 4, 2015 at 3:07 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Genevieve I just reran it locally and confirmed that the segments start at 230 for me, so I'm not sure what's going on. Still, maybe it meets your needs for now (but be aware that when we release V6 the segment numbering is likely to start at 230) cheers Bruce On Fri, 4 Dec 2015, UQAM wrote: Hi Bruce, We were using the correct mri_cc, but our segments were numbered 251 to 262 instead of 230 to 241 in the CColorLUT.txt. With this adjustment, the mri_cc now runs perfectly and segments in 12. Many thanks for your support! Best, Genevieve On Fri, Nov 27, 2015 at 3:58 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Genevieve are you sure you are using the correct mri_cc? I used your command line and got 12 segments. How many segents do you get? It should generate segments numbered 230-241 I think. You'll need to make your own entries in the ColorLUT.txt file if you want to see them in prespecified colors and names and such cheers Bruce On Fri, 27 Nov 2015, UQAM wrote: Hi Zeke, We tried the new version of mri_cc and we still do not get 12 segments of the corpus callosum when we open the aseg.12segmentsCC.mgz in a viewer. Could you send us the script you launch after the recon_all to get aseg.mgz files with 12 segments? basically the mri_cc Could you also please explain how to edit the ColorLut.txt file Finally, what is the precise script of the mri_segstats to generate stats tables. Thanks again, Cheers, Genevieve On Tue, Nov 24, 2015 at 11:20 PM, Z K <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>> wrote: Hello Genevieve, Below is a link to the newest version of mri_cc. Please copy it to your FREESURFER_HOME directory and backup the original. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_cc Hope this help. -Zeke On 11/24/2015 05:56 AM, UQAM wrote: Hi Bruce, DELL R910 Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 cores) 32 Go RAM CentOS release 5.10 (Final) kernel 2.6.18-371.3.1.el5 On Mon, Nov 23, 2015 at 7:32 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: Hi Genevieve I just tracked this down and it is a bug in mri_cc. If you tell Zeke your hardware/software environment he can get you a new version that should work cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi Bruce, Please find the two files attached. Genevieve On Mon, Nov 23, 2015 at 2:39 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: Hi Geneviève if you send us the $SUBJECTS_DIR/CColorLUT.txt and $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a look cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi, This a a "re-posting" of a question I've raised last week ; ) I would like to segment the corpus callosum into twelve even lenght segments instead of the five segments that freesurfer includes by default. - First I ran a mri_cc on subject e0070: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC.mgz -d 12 e0070 - Then I edited the ColorLUT.txt file and renamed it CColorLUT.txt (see attachment, segments 251 to 262). - Finally I ran a mri_segstats to compute the statistics on segmented volumes. mri_segstats seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 sum --e0070_CC12.aseg.stats The e0070_CC12.aseg.stats file still displays only five segments of the corpus callosum. Any tips or clues on how I could do things differently to get 12 segments? Thanks in advance, Geneviève _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
Hi Doug,
See attached an example of an aseg.stats file for subject e0070 ( e0070_CC12_new.aseg.stats)
Regards, Genevieve
On Mon, Dec 7, 2015 at 7:48 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Can you send me one of the e0070_CC12_new.aseg.stats files?
On 12/06/2015 08:12 AM, UQAM wrote:
Hi Bruce,
We used these:
mri_cc_new -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC_new.mgz -d 12 e0070 ... (for all the subjects from e0042 to a0040)
mri_segstats --seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC_new.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 --sum $SUBJECTS_DIR/e0070/stats/e0070_CC12_new.aseg.stats .... (for all the subjects from e0042 to a0040)
asegstats2table --subjects e0042 e0041 e0035 e0048 e0058 e0059 e0053 e0032 e0047 e0036 e0039 e0049 e0051 e0050 e0045 e0061 e0062 e0063 e0064 e0065 e0066 e0067 e0068 e0070 e0071 e0072 e0073 e0074 e0075 e0076 e0077 e0021 e0004 e0078 e0079 e0080 e0013 e0081 e0082 e0083 a0001 a0002 a0003 a0004 a0005 a0006 a0007 a0008 a0009 a0010 a0011 a0012 a0013 a0014 a0015 a0016 a0017 a0018 a0019 a0020 a0021 a0022 a0023 a0024 a0025 a0026 a0027 a0028 a0029 a0030 a0031 a0032 a0033 a0034 a0035 a0036 a0037 a0038 a0039 a0040 --meas volume --tablefile aseg_stats_12CC_new.txt
Genevieve
On Fri, Dec 4, 2015 at 5:56 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
HI Genevieve you'll need to send us all your command lines cheers Bruce On Fri, 4 Dec 2015, UQAM wrote: Hi again Bruce, The mri_cc & mri_segstats run just fine. - When I open the open the new segmented .mgz files (aseg.12segmentsCC_new.mgz) in tkmedit I can clearly visualize the 12 segments. - When I open the .stats file I get volumes for each of the 12 corpus callosum segments. However, when I run the asegstats2table the result is a .txt file with the usual 5 segments of the corpus callosum (anterior, ...). Any clue why the asegstats2table doesn't take into account the new 12 segments? See relevant files attached, As usual thanks so much ; ) Genevieve On Fri, Dec 4, 2015 at 3:07 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Genevieve I just reran it locally and confirmed that the segments start at 230 for me, so I'm not sure what's going on. Still, maybe it meets your needs for now (but be aware that when we release V6 the segment numbering is likely to start at 230) cheers Bruce On Fri, 4 Dec 2015, UQAM wrote: Hi Bruce, We were using the correct mri_cc, but our segments were numbered 251 to 262 instead of 230 to 241 in the CColorLUT.txt. With this adjustment, the mri_cc now runs perfectly and segments in 12. Many thanks for your support! Best, Genevieve On Fri, Nov 27, 2015 at 3:58 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Genevieve are you sure you are using the correct mri_cc? I used your command line and got 12 segments. How many segents do you get? It should generate segments numbered 230-241 I think. You'll need to make your own entries in the ColorLUT.txt file if you want to see them in prespecified colors and names and such cheers Bruce On Fri, 27 Nov 2015, UQAM wrote: Hi Zeke, We tried the new version of mri_cc and we still do not get 12 segments of the corpus callosum when we open the aseg.12segmentsCC.mgz in a viewer. Could you send us the script you launch after the recon_all to get aseg.mgz files with 12 segments? basically the mri_cc Could you also please explain how to edit the ColorLut.txt file Finally, what is the precise script of the mri_segstats to generate stats tables. Thanks again, Cheers, Genevieve On Tue, Nov 24, 2015 at 11:20 PM, Z K <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>> wrote: Hello Genevieve, Below is a link to the newest version of mri_cc. Please copy it to your FREESURFER_HOME directory and backup the original.ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_cc
Hope this help. -Zeke On 11/24/2015 05:56 AM, UQAM wrote: Hi Bruce, DELL R910 Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 cores) 32 Go RAM CentOS release 5.10 (Final) kernel 2.6.18-371.3.1.el5 On Mon, Nov 23, 2015 at 7:32 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: Hi Genevieve I just tracked this down and it is a bug in mri_cc. If you tell Zeke your hardware/software environment he can get you a new version that should work cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi Bruce, Please find the two files attached. Genevieve On Mon, Nov 23, 2015 at 2:39 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: Hi Geneviève if you send us the $SUBJECTS_DIR/CColorLUT.txt and $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a look cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi, This a a "re-posting" of a question I've raised last week ; ) I would like to segment the corpus callosum into twelve even lenght segments instead of the five segments that freesurfer includes by default. - First I ran a mri_cc on subject e0070: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC.mgz -d 12 e0070 - Then I edited the ColorLUT.txt file and renamed it CColorLUT.txt (see attachment, segments 251 to 262). - Finally I ran a mri_segstats to compute the statistics on segmented volumes. mri_segstats seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 sum --e0070_CC12.aseg.stats The e0070_CC12.aseg.stats file still displays only five segments of the corpus callosum. Any tips or clues on how I could do things differently to get 12 segments? Thanks in advance, Geneviève _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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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/
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Hi Doug, Hi Bruce,
Just an update.
I tried this command (see below) to specify each input file since I don't want to freesurfer to choose the stats/aseg.stats that it uses by default.
but I get this "ERROR: The stats file e0042/stats/e0042_CC12_new.aseg.stats is not found or is too small to be a valid statsfile".
The files are indeed in the stats folder of subject e0042, but the default aseg.stats files are 8,5K and my CC_new.aseg.stats files are 4,5K.
Hope it can help to solve the problem ; )
Genevieve
* * *
asegstats2table -i e0042/stats/e0042_CC12_new.aseg.stats e0041/stats/e0041_CC12_new.aseg.stats e0035/stats/e0035_CC12_new.aseg.stats e0048/stats/e0048_CC12_new.aseg.stats e0058/stats/e0058_CC12_new.aseg.stats e0059/stats/e0059_CC12_new.aseg.stats e0053/stats/e0053_CC12_new.aseg.stats e0032/stats/e0032_CC12_new.aseg.stats e0047/stats/e0047_CC12_new.aseg.stats e0036/stats/e0036_CC12_new.aseg.stats e0039/stats/e0039_CC12_new.aseg.stats e0049/stats/e0049_CC12_new.aseg.stats e0051/stats/e0051_CC12_new.aseg.stats e0050/stats/e0050_CC12_new.aseg.stats e0045/stats/e0045_CC12_new.aseg.stats e0061/stats/e0061_CC12_new.aseg.stats e0062/stats/e0062_CC12_new.aseg.stats e0063/stats/e0063_CC12_new.aseg.stats e0064/stats/e0064_CC12_new.aseg.stats e0065/stats/e0065_CC12_new.aseg.stats e0066/stats/e0066_CC12_new.aseg.stats e0067/stats/e0067_CC12_new.aseg.stats e0068/stats/e0068_CC12_new.aseg.stats e0070/stats/e0070_CC12_new.aseg.stats e0071/stats/e0071_CC12_new.aseg.stats e0072/stats/e0072_CC12_new.aseg.stats e0073/stats/e0073_CC12_new.aseg.stats e0074/stats/e0074_CC12_new.aseg.stats e0075/stats/e0075_CC12_new.aseg.stats e0076/stats/e0076_CC12_new.aseg.stats e0077/stats/e0077_CC12_new.aseg.stats e0021/stats/e0021_CC12_new.aseg.stats e0004/stats/e0004_CC12_new.aseg.stats e0078/stats/e0078_CC12_new.aseg.stats e0079/stats/e0079_CC12_new.aseg.stats e0080/stats/e0080_CC12_new.aseg.stats e0013/stats/e0013_CC12_new.aseg.stats e0081/stats/e0081_CC12_new.aseg.stats e0082/stats/e0082_CC12_new.aseg.stats e0083/stats/e0083_CC12_new.aseg.stats a0001/stats/a0001_CC12_new.aseg.stats a0002/stats/a0002_CC12_new.aseg.stats a0003/stats/a0003_CC12_new.aseg.stats a0004/stats/a0004_CC12_new.aseg.stats a0005/stats/a0005_CC12_new.aseg.stats a0006/stats/a0006_CC12_new.aseg.stats a0007/stats/a0007_CC12_new.aseg.stats a0008/stats/a0008_CC12_new.aseg.stats a0009/stats/a0009_CC12_new.aseg.stats a0010/stats/a0010_CC12_new.aseg.stats a0011/stats/a0011_CC12_new.aseg.stats a0012/stats/a0012_CC12_new.aseg.stats a0013/stats/a0013_CC12_new.aseg.stats a0014/stats/a0014_CC12_new.aseg.stats a0015/stats/a0015_CC12_new.aseg.stats a0016/stats/a0016_CC12_new.aseg.stats a0017/stats/a0017_CC12_new.aseg.stats a0018/stats/a0018_CC12_new.aseg.stats a0019/stats/a0019_CC12_new.aseg.stats a0020/stats/a0020_CC12_new.aseg.stats a0021/stats/a0021_CC12_new.aseg.stats a0022/stats/a0022_CC12_new.aseg.stats a0023/stats/a0023_CC12_new.aseg.stats a0024/stats/a0024_CC12_new.aseg.stats a0025/stats/a0025_CC12_new.aseg.stats a0026/stats/a0026_CC12_new.aseg.stats a0027/stats/a0027_CC12_new.aseg.stats a0028/stats/a0028_CC12_new.aseg.stats a0029/stats/a0029_CC12_new.aseg.stats a0030/stats/a0030_CC12_new.aseg.stats a0031/stats/a0031_CC12_new.aseg.stats a0032/stats/a0032_CC12_new.aseg.stats a0033/stats/a0033_CC12_new.aseg.stats a0034/stats/a0034_CC12_new.aseg.stats a0035/stats/a0035_CC12_new.aseg.stats a0036/stats/a0036_CC12_new.aseg.stats a0037/stats/a0037_CC12_new.aseg.stats a0038/stats/a0038_CC12_new.aseg.stats a0039/stats/a0039_CC12_new.aseg.stats a0040/stats/a0040_CC12_new.aseg.stats --meas volume --tablefile aseg_stats_12CC_new.txt
On Tue, Dec 8, 2015 at 6:40 AM, UQAM allaire-duquette.genevieve@uqam.ca wrote:
Hi Doug,
See attached an example of an aseg.stats file for subject e0070 ( e0070_CC12_new.aseg.stats)
Regards, Genevieve
On Mon, Dec 7, 2015 at 7:48 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Can you send me one of the e0070_CC12_new.aseg.stats files?
On 12/06/2015 08:12 AM, UQAM wrote:
Hi Bruce,
We used these:
mri_cc_new -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC_new.mgz -d 12 e0070 ... (for all the subjects from e0042 to a0040)
mri_segstats --seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC_new.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 --sum $SUBJECTS_DIR/e0070/stats/e0070_CC12_new.aseg.stats .... (for all the subjects from e0042 to a0040)
asegstats2table --subjects e0042 e0041 e0035 e0048 e0058 e0059 e0053 e0032 e0047 e0036 e0039 e0049 e0051 e0050 e0045 e0061 e0062 e0063 e0064 e0065 e0066 e0067 e0068 e0070 e0071 e0072 e0073 e0074 e0075 e0076 e0077 e0021 e0004 e0078 e0079 e0080 e0013 e0081 e0082 e0083 a0001 a0002 a0003 a0004 a0005 a0006 a0007 a0008 a0009 a0010 a0011 a0012 a0013 a0014 a0015 a0016 a0017 a0018 a0019 a0020 a0021 a0022 a0023 a0024 a0025 a0026 a0027 a0028 a0029 a0030 a0031 a0032 a0033 a0034 a0035 a0036 a0037 a0038 a0039 a0040 --meas volume --tablefile aseg_stats_12CC_new.txt
Genevieve
On Fri, Dec 4, 2015 at 5:56 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
HI Genevieve you'll need to send us all your command lines cheers Bruce On Fri, 4 Dec 2015, UQAM wrote: Hi again Bruce, The mri_cc & mri_segstats run just fine. - When I open the open the new segmented .mgz files (aseg.12segmentsCC_new.mgz) in tkmedit I can clearly visualize the 12 segments. - When I open the .stats file I get volumes for each of the 12 corpus callosum segments. However, when I run the asegstats2table the result is a .txt file with the usual 5 segments of the corpus callosum (anterior, ...). Any clue why the asegstats2table doesn't take into account the new 12 segments? See relevant files attached, As usual thanks so much ; ) Genevieve On Fri, Dec 4, 2015 at 3:07 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Genevieve I just reran it locally and confirmed that the segments start at 230 for me, so I'm not sure what's going on. Still, maybe it meets your needs for now (but be aware that when we release V6 the segment numbering is likely to start at 230) cheers Bruce On Fri, 4 Dec 2015, UQAM wrote: Hi Bruce, We were using the correct mri_cc, but our segments were numbered 251 to 262 instead of 230 to 241 in the CColorLUT.txt. With this adjustment, the mri_cc now runs perfectly and segments in 12. Many thanks for your support! Best, Genevieve On Fri, Nov 27, 2015 at 3:58 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.eduwrote: Hi Genevieve are you sure you are using the correct mri_cc? I used your command line and got 12 segments. How many segents do you get? It should generate segments numbered 230-241 I think. You'll need to make your own entries in the ColorLUT.txt file if you want to see them in prespecified colors and names and such cheers Bruce On Fri, 27 Nov 2015, UQAM wrote: Hi Zeke, We tried the new version of mri_cc and we still do not get 12 segments of the corpus callosum when we open the aseg.12segmentsCC.mgz in a viewer. Could you send us the script you launch after the recon_all to get aseg.mgz files with 12 segments? basically the mri_cc Could you also please explain how to edit the ColorLut.txt file Finally, what is the precise script of the mri_segstats to generate stats tables. Thanks again, Cheers, Genevieve On Tue, Nov 24, 2015 at 11:20 PM, Z K <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>> wrote: Hello Genevieve, Below is a link to the newest version of mri_cc. Please copy it to your FREESURFER_HOME directory and backup the original.ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_cc
Hope this help. -Zeke On 11/24/2015 05:56 AM, UQAMwrote:
Hi Bruce, DELL R910 Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 cores) 32 Go RAM CentOS release 5.10 (Final) kernel 2.6.18-371.3.1.el5 On Mon, Nov 23, 2015 at 7:32 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: Hi Genevieve I just tracked this down and it is a bug in mri_cc. If you tell Zeke your hardware/software environment he can get you a new version that should work cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi Bruce, Please find the two files attached. Genevieve On Mon, Nov 23, 2015 at 2:39 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: Hi Geneviève if you send us the $SUBJECTS_DIR/CColorLUT.txt and $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a look cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi, This a a "re-posting" of a question I've raised last week ; ) I would like to segment the corpus callosum into twelve even lenght segments instead of the five segments that freesurfer includes by default. - First I ran a mri_cc on subject e0070: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC.mgz -d 12 e0070 - Then I edited the ColorLUT.txt file and renamed it CColorLUT.txt(see
attachment, segments 251 to 262). - Finally I ran a mri_segstats to compute the statistics on segmented volumes. mri_segstats seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 sum --e0070_CC12.aseg.stats The e0070_CC12.aseg.stats file still displays only five segments of the corpus callosum. Any tips or clues on how I could do things differently to get 12 segments? Thanks in advance, Geneviève _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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-- 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/
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