Re: [Freesurfer] Computing SA from an older FS version
Hi Niels
the matlab commands should be:
[v, M,mr] = load_mgh('wm.mgz') ;
save_mgh(v, 'wm.mgz', M,mr);
cheers
Bruce
On Mon, 13 Jul 2015, Gerrits, Niels
wrote:
Dear Bruce,
Thanks for the quick reply! I think it might be possible that we used an
unrelased or developmental version of FreeSurfer, because the building-stamp
said: freesurfer-Linux-centos5_86_64_dev-20110315. I’m not sure how this
version ended up onto the server I was working on. Do you think this is a
problem?
With respect to the error: you were right, it was longer. I copied the
command line below:
$ mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f
stats/lh.aparc.pial.stats -b -a label/lh.aparc.annot -c
label/aparc.annot.ctab 0007 lh pial
INFO: assuming MGZ format for volumes.
INFO: using label/lh.cortex.label as mask to calc cortex NumVert, SurfArea
and MeanThickness. computing statistics for each annotation in
label/lh.aparc.annot. reading
volume/data2/projects/ysbrand-vumc/pddatabase-freesurfer/niels_test//0007/mri/wm.
mgz... znzTAGskip: tag=825050957, failed to calloc 1969843200 bytes!
I then loaded wm.mgh into matlab and then saved it as you suggested and ran
the command again to calculate SA of the pial surface, but it produces the
exact same error…
load.mgh wm.mgz;
save.mgh wm.mgz;
Am I doing anything wrong?
Thanks again!
Cheers,
Niels
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: zondag 12 juli 2015 16:44
To: Freesurfer support list
Subject: Re: [Freesurfer] Computing SA from an older FS version
Hi Niels
is that the entire error? Does it not say what volume produces the error?
That was a bug we had briefly some time ago, but I didn't think it made it
into anything we released. If you can track down which volume is causing
this problem you can just load it into matlab with load_mgh.m then save it
with save_mgh.m and the error will go away (since the matlab code doesn't
try to read or write the tagged information). Make sure to save all the
volumes that you do this to somewhere before overwriting them.
cheers
Bruce
On
Sun, 12 Jul 2015, Gerrits, Niels wrote:
Dear FreeSurfer-experts,
Unfortunately, nobody replied to my question so this is a repost (see the
original question below). Could anybody please give some advise on how to
proceed? The deadline for the revisions is drawing near, so any help is
greatly appreciated!
Best wishes,
Niels
---
-
Dear FreeSurfer-experts,
In 2012 I used a (currently outdated) version of FreeSurfer to analyze my
data on an external server and wrote an article about our findings. Now
the
reviewers asked us to recalculate surface area using the pial surface,
instead of the WM/GM boundary. I found the command on the mailing list to
do
so, but I got an error, which is probably related to the fact that there
is
a new version of FreeSurfer installed on the server and that the old
version
has been deleted.
Command to obtain SA from the pial surface:
mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f
stats/lh.aparc.pial.stats -b –a label/lh.aparc.annot -c
label/aparc.annot.ctab subject lh pial
Error:
znzTAGskip: tag=825050957, failed to alloc 1969843200 bytes!
Cannot allocate memory!
Now I have two questions:
1) When trying to find in which version of FreeSurfer the existing files
were created, I checked both the build-stamp.txt file and the
recon-all.log
file, and both say that the version of Freesurfer that was used was
freesurfer-Linux-centos5_86_64_dev-20110315. Is this an actual version? I
cannot find anything on the Internet about it. If not, what version could
this have been?
2) I understood that running two different versions of FreeSurfer on the
same data is not favourable. However, the numbers we are looking for are
already computed and now we only need to get them out of the existing
files.
Do you have any advice on how to do that?
Running recon-all again using the new version (5.3) does not seem to be an
option, since manual edits were made during the preprocessing. It is
therefore likely that we will obtain different results when compared with
our current findings when running recon-all again using the new version,
and
we would have to rewrite our entire article.
Any help is greatly appreciated!
Best wishes,
Niels Gerrits
___
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Re: [Freesurfer] Regarding: Brainstem substructures
Hi Sampada, FS 6.0 is not out yet, but you can download the latest dev version from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ Using this version, you can run the brainstem module on subjects that have already been processed with 5.3. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Dr Sampada Sinha drsampadasi...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Saturday, July 11, 2015 6:37:12 PM Subject: Re: [Freesurfer] Regarding: Brainstem substructures Thanks so much Bruce for your reply. when I open the link for brain stem structures ( https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures ), it says This functionality is present in FreeSurfer 6.0 and later . And, when I go to the freesurfer download page, the only latest version of freesurfer (last updated by Zeke on 2015-06-02) I see is stable v5.3.0. If the version 6.0 is out, will you please send me the link so that I can download it? Thanks and regards, Sampada On Sat, Jul 11, 2015 at 7:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Sampada the brainstem stuff was developed after 5.3 so it is likely not in the version you have. Eugenio or Zeke can point you in the right direction. cheers Bruce On Sat, 11 Jul 2015, Dr Sampada Sinha wrote: Dear freesurfer experts, I am trying to do the brainstem volumetric analysis especially of the medullary region. My recon-all command ran successfully and now when I am trying to run the command ' recon-all -s IMRAN -brainstem-structures' ( https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures ) but, I get the following error: ERROR: Flag -brainstem-structures unrecognized. -s IMRAN -brainstem-structures Linux localhost.localdomain 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Will you please let me know where I am going wrong? I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 version for my analysis. Thanks for your time! Kind regards, Sampada ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Computing SA from an older FS version
Dear Bruce, Thanks for the quick reply! I think it might be possible that we used an unrelased or developmental version of FreeSurfer, because the building-stamp said: freesurfer-Linux-centos5_86_64_dev-20110315. I'm not sure how this version ended up onto the server I was working on. Do you think this is a problem? With respect to the error: you were right, it was longer. I copied the command line below: $ mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f stats/lh.aparc.pial.stats -b -a label/lh.aparc.annot -c label/aparc.annot.ctab 0007 lh pial INFO: assuming MGZ format for volumes. INFO: using label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. computing statistics for each annotation in label/lh.aparc.annot. reading volume /data2/projects/ysbrand-vumc/pddatabase-freesurfer/niels_test//0007/mri/wm.mgz... znzTAGskip: tag=825050957, failed to calloc 1969843200 bytes! I then loaded wm.mgh into matlab and then saved it as you suggested and ran the command again to calculate SA of the pial surface, but it produces the exact same error... load.mgh wm.mgz; save.mgh wm.mgz; Am I doing anything wrong? Thanks again! Cheers, Niels -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: zondag 12 juli 2015 16:44 To: Freesurfer support list Subject: Re: [Freesurfer] Computing SA from an older FS version Hi Niels is that the entire error? Does it not say what volume produces the error? That was a bug we had briefly some time ago, but I didn't think it made it into anything we released. If you can track down which volume is causing this problem you can just load it into matlab with load_mgh.m then save it with save_mgh.m and the error will go away (since the matlab code doesn't try to read or write the tagged information). Make sure to save all the volumes that you do this to somewhere before overwriting them. cheers Bruce On Sun, 12 Jul 2015, Gerrits, Niels wrote: Dear FreeSurfer-experts, Unfortunately, nobody replied to my question so this is a repost (see the original question below). Could anybody please give some advise on how to proceed? The deadline for the revisions is drawing near, so any help is greatly appreciated! Best wishes, Niels --- - Dear FreeSurfer-experts, In 2012 I used a (currently outdated) version of FreeSurfer to analyze my data on an external server and wrote an article about our findings. Now the reviewers asked us to recalculate surface area using the pial surface, instead of the WM/GM boundary. I found the command on the mailing list to do so, but I got an error, which is probably related to the fact that there is a new version of FreeSurfer installed on the server and that the old version has been deleted. Command to obtain SA from the pial surface: mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f stats/lh.aparc.pial.stats -b -a label/lh.aparc.annot -c label/aparc.annot.ctab subject lh pial Error: znzTAGskip: tag=825050957, failed to alloc 1969843200 bytes! Cannot allocate memory! Now I have two questions: 1) When trying to find in which version of FreeSurfer the existing files were created, I checked both the build-stamp.txt file and the recon-all.log file, and both say that the version of Freesurfer that was used was freesurfer-Linux-centos5_86_64_dev-20110315. Is this an actual version? I cannot find anything on the Internet about it. If not, what version could this have been? 2) I understood that running two different versions of FreeSurfer on the same data is not favourable. However, the numbers we are looking for are already computed and now we only need to get them out of the existing files. Do you have any advice on how to do that? Running recon-all again using the new version (5.3) does not seem to be an option, since manual edits were made during the preprocessing. It is therefore likely that we will obtain different results when compared with our current findings when running recon-all again using the new version, and we would have to rewrite our entire article. Any help is greatly appreciated! Best wishes, Niels Gerrits ___ 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
Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation
Hi Eugenio, I have a question about hippocampal segmentation. Do you think it is possible to use this segmentation to obtain specific seeds for a functional connectivity study? thank you Angela Sorry, I forgot to mention that you should change the permissions of the files. Please run the following command: chmod u+x $FREESURFER_HOME/bin/run_segmentSubject*.sh Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 1:07:31 PM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Thank you Eugenio, but the problem is still present (attached the log). Thank you for any help! Angela #@# Hippocampal Subfields processing (T1 only) left Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects left \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. # #@# Hippocampal Subfields processing (T1 only) right Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects right \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. #-- Started at Wed Jul 1 13:04:45 CEST 2015 Ended at Wed Jul 1 13:04:47 CEST 2015 #@#%# recon-all-run-time-hours 0.001 recon-all -s subj001 finished without error at Wed Jul 1 13:04:47 CEST 2015 Hi Angela, I think this is a problem I fixed in the development version a couple of days ago. Can you please just try saving the attached 3 files in the directory $FREESURFER_HOME/bin/ replacing the ones that are there? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 5:42:07 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi all, I have tried to run the new hippocampal segmentation module (after running the dev version of FS 6. The module did not work and this message error appears (please find attached the log). DYLD_LIBRARY_PATH is /Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/runtime/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/bin/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/sys/os/maci64 Warning: application is running on a locale different from the original platform locale. is it due to something wrong in my path specification? how can I solve this? thank you! Angela Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own experience using it, specifically the Hippocampal subfield segmentation protocol. Are people receiving any unusual errors? Is there a lower resolution or less accurate segmentation of other cortical or subcortical structures? Any input would be great. Cheers, Noah Markowitz ___ 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
Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation
Hi Angela, Of course it is! I'd be thrilled to see what you get out of your analyses; please keep me posted. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Monday, July 13, 2015 11:21:30 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi Eugenio, I have a question about hippocampal segmentation. Do you think it is possible to use this segmentation to obtain specific seeds for a functional connectivity study? thank you Angela Sorry, I forgot to mention that you should change the permissions of the files. Please run the following command: chmod u+x $FREESURFER_HOME/bin/run_segmentSubject*.sh Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 1:07:31 PM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Thank you Eugenio, but the problem is still present (attached the log). Thank you for any help! Angela #@# Hippocampal Subfields processing (T1 only) left Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects left \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. # #@# Hippocampal Subfields processing (T1 only) right Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects right \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. #-- Started at Wed Jul 1 13:04:45 CEST 2015 Ended at Wed Jul 1 13:04:47 CEST 2015 #@#%# recon-all-run-time-hours 0.001 recon-all -s subj001 finished without error at Wed Jul 1 13:04:47 CEST 2015 Hi Angela, I think this is a problem I fixed in the development version a couple of days ago. Can you please just try saving the attached 3 files in the directory $FREESURFER_HOME/bin/ replacing the ones that are there? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 5:42:07 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi all, I have tried to run the new hippocampal segmentation module (after running the dev version of FS 6. The module did not work and this message error appears (please find attached the log). DYLD_LIBRARY_PATH is /Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/runtime/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/bin/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/sys/os/maci64 Warning: application is running on a locale different from the original platform locale. is it due to something wrong in my path specification? how can I solve this? thank you! Angela Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own
Re: [Freesurfer] cortical reconstruction problem
Hi Bruce, Many thanks for your answer. Best, Mohamed On 10/07/15 15:29, Bruce Fischl wrote: Hi Mohamed what you are showing is *not* the cortical reconstruction, but rather the whole-brain segmentation/aseg. Have you looked at the ?h.white and ?h.pial surfaces? We use them for cortical modeling as they are frequently more accurate than the aseg. cheers Bruce On Fri, 10 Jul 2015, Mohamed Ali Bahri wrote: Dear Experts, Cortical reconstruction (mri-segmentation) does not work well for some of my subjects. The segmentation missed a part of the GM (see attached figure). I am wandering if the expert options could help. Any suggestions/comments will be very welcome. Many thanks in advance, Mohamed ___ 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. -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Cyclotron Research Centre, University of Liège, Belgium m.ba...@ulg.ac.be ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Computing SA from an older FS version
Hi Bruce,
Thank you so much and I'm sorry for the newbie question(s). It's working now!
Cheers,
Niels
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: maandag 13 juli 2015 14:46
To: Freesurfer support list
Subject: Re: [Freesurfer] Computing SA from an older FS version
Hi Niels
the matlab commands should be:
[v, M,mr] = load_mgh('wm.mgz') ;
save_mgh(v, 'wm.mgz', M,mr);
cheers
Bruce
On Mon, 13 Jul 2015, Gerrits, Niels
wrote:
Dear Bruce,
Thanks for the quick reply! I think it might be possible that we used an
unrelased or developmental version of FreeSurfer, because the building-stamp
said: freesurfer-Linux-centos5_86_64_dev-20110315. I'm not sure how this
version ended up onto the server I was working on. Do you think this is a
problem?
With respect to the error: you were right, it was longer. I copied the
command line below:
$ mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f
stats/lh.aparc.pial.stats -b -a label/lh.aparc.annot -c
label/aparc.annot.ctab 0007 lh pial
INFO: assuming MGZ format for volumes.
INFO: using label/lh.cortex.label as mask to calc cortex NumVert, SurfArea
and MeanThickness. computing statistics for each annotation in
label/lh.aparc.annot. reading
volume/data2/projects/ysbrand-vumc/pddatabase-freesurfer/niels_test//0007/mri/wm.
mgz... znzTAGskip: tag=825050957, failed to calloc 1969843200 bytes!
I then loaded wm.mgh into matlab and then saved it as you suggested and ran
the command again to calculate SA of the pial surface, but it produces the
exact same error...
load.mgh wm.mgz;
save.mgh wm.mgz;
Am I doing anything wrong?
Thanks again!
Cheers,
Niels
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: zondag 12 juli 2015 16:44
To: Freesurfer support list
Subject: Re: [Freesurfer] Computing SA from an older FS version
Hi Niels
is that the entire error? Does it not say what volume produces the error?
That was a bug we had briefly some time ago, but I didn't think it made it
into anything we released. If you can track down which volume is causing
this problem you can just load it into matlab with load_mgh.m then save it
with save_mgh.m and the error will go away (since the matlab code doesn't
try to read or write the tagged information). Make sure to save all the
volumes that you do this to somewhere before overwriting them.
cheers
Bruce
On
Sun, 12 Jul 2015, Gerrits, Niels wrote:
Dear FreeSurfer-experts,
Unfortunately, nobody replied to my question so this is a repost (see the
original question below). Could anybody please give some advise on how to
proceed? The deadline for the revisions is drawing near, so any help is
greatly appreciated!
Best wishes,
Niels
---
-
Dear FreeSurfer-experts,
In 2012 I used a (currently outdated) version of FreeSurfer to analyze my
data on an external server and wrote an article about our findings. Now
the
reviewers asked us to recalculate surface area using the pial surface,
instead of the WM/GM boundary. I found the command on the mailing list to
do
so, but I got an error, which is probably related to the fact that there
is
a new version of FreeSurfer installed on the server and that the old
version
has been deleted.
Command to obtain SA from the pial surface:
mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f
stats/lh.aparc.pial.stats -b -a label/lh.aparc.annot -c
label/aparc.annot.ctab subject lh pial
Error:
znzTAGskip: tag=825050957, failed to alloc 1969843200 bytes!
Cannot allocate memory!
Now I have two questions:
1) When trying to find in which version of FreeSurfer the existing files
were created, I checked both the build-stamp.txt file and the
recon-all.log
file, and both say that the version of Freesurfer that was used was
freesurfer-Linux-centos5_86_64_dev-20110315. Is this an actual version? I
cannot find anything on the Internet about it. If not, what version could
this have been?
2) I understood that running two different versions of FreeSurfer on the
same data is not favourable. However, the numbers we are looking for are
already computed and now we only need to get them out of the existing
files.
Do you have any advice on how to do that?
Running recon-all again using the new version (5.3) does not seem to be an
option,
Re: [Freesurfer] Computing SA from an older FS version
no worries, glad to hear we sorted it out
Bruce
On Mon, 13 Jul 2015, Gerrits,
Niels wrote:
Hi Bruce,
Thank you so much and I’m sorry for the newbie question(s). It’s working
now!
Cheers,
Niels
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: maandag 13 juli 2015 14:46
To: Freesurfer support list
Subject: Re: [Freesurfer] Computing SA from an older FS version
Hi Niels
the matlab commands should be:
[v, M,mr] = load_mgh('wm.mgz') ;
save_mgh(v, 'wm.mgz', M,mr);
cheers
Bruce
On Mon, 13 Jul 2015, Gerrits, Niels
wrote:
Dear Bruce,
Thanks for the quick reply! I think it might be possible that we used an
unrelased or developmental version of FreeSurfer, because the
building-stamp
said: freesurfer-Linux-centos5_86_64_dev-20110315. I’m not sure how this
version ended up onto the server I was working on. Do you think this is a
problem?
With respect to the error: you were right, it was longer. I copied the
command line below:
$ mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f
stats/lh.aparc.pial.stats -b -a label/lh.aparc.annot -c
label/aparc.annot.ctab 0007 lh pial
INFO: assuming MGZ format for volumes.
INFO: using label/lh.cortex.label as mask to calc cortex NumVert, SurfArea
and MeanThickness. computing statistics for each annotation in
label/lh.aparc.annot. reading
volume/data2/projects/ysbrand-vumc/pddatabase-freesurfer/niels_test//0007/m
ri/wm.
mgz... znzTAGskip: tag=825050957, failed to calloc 1969843200 bytes!
I then loaded wm.mgh into matlab and then saved it as you suggested and
ran
the command again to calculate SA of the pial surface, but it produces the
exact same error…
load.mgh wm.mgz;
save.mgh wm.mgz;
Am I doing anything wrong?
Thanks again!
Cheers,
Niels
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: zondag 12 juli 2015 16:44
To: Freesurfer support list
Subject: Re: [Freesurfer] Computing SA from an older FS version
Hi Niels
is that the entire error? Does it not say what volume produces the error?
That was a bug we had briefly some time ago, but I didn't think it made it
into anything we released. If you can track down which volume is causing
this problem you can just load it into matlab with load_mgh.m then save it
with save_mgh.m and the error will go away (since the matlab code doesn't
try to read or write the tagged information). Make sure to save all the
volumes that you do this to somewhere before overwriting them.
cheers
Bruce
On
Sun, 12 Jul 2015, Gerrits, Niels wrote:
Dear FreeSurfer-experts,
Unfortunately, nobody replied to my question so this is a repost (see
the
original question below). Could anybody please give some advise on how
to
proceed? The deadline for the revisions is drawing near, so any help is
greatly appreciated!
Best wishes,
Niels
--
-
-
Dear FreeSurfer-experts,
In 2012 I used a (currently outdated) version of FreeSurfer to analyze
my
data on an external server and wrote an article about our findings. Now
the
reviewers asked us to recalculate surface area using the pial surface,
instead of the WM/GM boundary. I found the command on the mailing list
to
do
so, but I got an error, which is probably related to the fact that there
is
a new version of FreeSurfer installed on the server and that the old
version
has been deleted.
Command to obtain SA from the pial surface:
mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f
stats/lh.aparc.pial.stats -b –a label/lh.aparc.annot -c
label/aparc.annot.ctab subject lh pial
Error:
znzTAGskip: tag=825050957, failed to alloc 1969843200 bytes!
Cannot allocate memory!
Now I have two questions:
1) When trying to find in which version of FreeSurfer the existing files
were created, I checked both the build-stamp.txt file and the
recon-all.log
file, and both say that the version of Freesurfer that was used was
freesurfer-Linux-centos5_86_64_dev-20110315. Is this an actual version?
I
cannot find anything on the Internet about it. If not, what version
could
this have been?
2) I understood that running two different versions of FreeSurfer on the
same data is not favourable. However, the numbers we are looking for are
already computed and now we only need to get them out of the existing
[Freesurfer] Tracula - set echo spacing
Hi Anastasia and Tracula experts, We are running a new set of tracula analysis from Bay 6 and are wondering how do we define the number of echo spacing in the dmrirc file. Is it a number that we get from the header of the field map dicoms? set echospacing = ... Thanks a lot Celine -- Celine Louapre, MD, PhD Research Fellow at Massachusetts General Hospital Multiple Sclerosis Imaging Lab AA Martinos Center for Biomedical Imaging Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129, USA ___ 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] Hippocampal sufields in MNI templates
Dear freesurfer users,I was wondering: is there any way to get normalized ROIs for hippocampal subfields in MNI space? Is anything speaking against for example, running freesurfer with subcortical segmentation on an MNI template? cheers and kind regards, Lorenzo Pasquini___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_tessellate: max vertices 1000000 exceeded
Hello, Here is a download link to the most recent version of mri_tessellate: ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_tessellate Please place the new version in your $FREESURFER_HOME/bin directory, and backup the original. Hope this helps. -Zeke FREESURFER_HOME: /usr/local/freesurfer/stable5_3 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: 7.6 Kernel info: Linux 3.2.0-4-amd64 x86_64 I think the info was at the end of the original email, as per instructions. I'm guessing it was just hidden, but let me know if there's any other info you need? Thanks! Ione -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Saturday, July 11, 2015 3:01 PM To: ionef...@uw.edu; Freesurfer support list Subject: Re: [Freesurfer] mri_tessellate: max vertices 100 exceeded Hi Iona if you tell us what your hardware/software environment is we'll get you a newer version. cheers Bruce On Sat, 11 Jul 2015, Ione Fine wrote: Hi, I am running to an error analyzing a 0.5 mm resolution T1 structural with the following with the following: recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT the issue seems to be: mri_tessellate: max vertices 100 exceeded There?s apparently a version of mri_tesselate which is easier going about the number of vertices, but the link to it is broken. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-August/0400 01.html Thanks Ione System information: FREESURFER_HOME: /usr/local/freesurfer/stable5_3 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: 7.6 Kernel info: Linux 3.2.0-4-amd64 x86_64 Professor of Psychology University of Washington http://faculty.washington.edu/ionefine/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Fwd: [FreeSurfer] aparc+aseg.mgz unkown voxels
Hello, Just checking if this email thread was still being tracked. Thanks so much Joseph -- Forwarded message -- From: joseph veliz josephveli...@gmail.com Date: Thu, Jul 9, 2015 at 10:41 AM Subject: Re: [Freesurfer] [FreeSurfer] aparc+aseg.mgz unkown voxels To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu I have updated our macbook 10.9 with the latest freesurfer from; ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Darwin-lion-dev.tar.gz The same results are produced; ' unknown voxels ' on the aparc+aseg.mgz. I am not sure how to proceed, are there any suggestions? thank you so much joseph On Thu, Jul 2, 2015 at 12:45 PM, joseph veliz josephveli...@gmail.com wrote: We have quite a large data set we have processed in this study on v5.1.0 and have been previously advised to not switch versions in-between processing data sets. I do have a macbook pro running v5.3, I will attempt to recon on this subject. But are there any other options on v5.1? Why is it that voxels in aparc+aseg.mgz can not just be filled in with corresponding color from the lut? On Thu, Jul 2, 2015 at 6:04 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I think that might have been fixed in 5.3. Can you try 5.3 on that one subject to see? Thanks for the kudos. doug On 07/01/2015 08:23 PM, joseph veliz wrote: leopard i686 stable pub v5.1.0 As an aside I watched your introductory videos and found you to be very knowledgeable, well-spoken and very helpful in understanding some of the amazing things you guys are doing for analysis. Really cool to be emailing you and getting help from the pros. Thanks Joe On Wed, Jul 1, 2015 at 1:12 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Joe what FS version are you using? That certainly looks like a bug, but maybe it's one we've fixed already? Bruce On Wed, 1 Jul 2015, joseph veliz wrote: Hello Freesrufers, There are voxels in random areas of the aparc+aseg.mgz that are categorized as 'unknown'. I read an earlier email stating that aparc+aseg.mgz should not be directly edited by filling in voxels. Correct? A specific example of this is shown on the attatched images. aseg.mgz categorizes this area as cortex, yet the aparc+aseg.mgz does not even though it is within pial boundary and is adjacent to other (categorized) cortical and sub cortical regions. How could we go about correcting this? Thank so much Joe ___ 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity
Hi list, When I use tkmedit the overlap between orig and ROI_MASK.nii.gz seem to correspond. However, when I added the ROI_MASK.nii.gz, the orig is vanished, and is remained the ROI_MASK in correct position (and in white) and around all black. My concern is the correct binarization of ROI_MASK which it seem correct when I use fslview.fslview orig.nii.gz ROI_MASK.nii.gz produce perfect outputs. After mri_label2vol --seg $SUBJECTS_DIR/ROI_MASK.nii.gz --reg $FUNCTIONAL_DATA/Sess102/rest/001/register.dof6.dat --temp $FUNCTIONAL_DATA/Sess102/rest/001/template.nii.gz --fillthresh 0.5 --o func.vmPFC_MASK.nii The func.vmPFC_MASK.nii (344MB) seem to be empty when I open it with tkmedit and too big (a red bar which cover the whole) when I use fslview.With MRIcron, is screen is irregularly divided in half in black and white. Which should be the advised folder for func.vmPFC_MASK.nii? Thank you very much Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 30-giu-2015 0.36 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity Hi Stefano, sorry for the delay, I was traveling. It sounds like you just need to run fcseed-config and specify -seg ROI_MASK.mgz and -segid 1 (assuming your ROI_MASK is in $SUBJECTS_DIR/subject/mri). If the mask is in the orig.mgz space, then everything should work ok, but you can look at it with tkmedit -f orig.mgz -aux ROI_MASK.mgz You can also run mri_label2vol --seg $SUBJECTS_DIR/subject/mri/ROI_MASK.mgz --reg register.dof6.dat --temp template.nii.gz --fillthresh 0.5 --o func.ROI_MASK.nii where template.nii.gz and register.dof6.dat are in the functional run folder doug On 06/12/2015 04:39 PM, std...@virgilio.it wrote: Hi list, I working on the combination of MRS and FS-FAST analysis. I have extracted the grey matter within voxel (I will call it ROI_MASK) by using FSL tools and now it is in the same space of orig.mgz (the roi mask is perfectly overlapped on orig.nii.gz when I use fslview). I'd like to import it to FS for performing seed-based FS-FAST functional connectivity. The seed should the ROI MASK (GM within voxel). I know that the FSL and FS operate in different space and orientation. I think to have resolved the problem of different space by using orig.nii.gz to create ROI mask by FSL. However, I'm strongly worried for orientation issues. I have read the guidelines in FSL and FS sites, but I'm quite confused. In detail, I'd like to ask whether I should use mri_cor2label to transform ROI mask created by FSL to label. Furthmore, I'd like to be sure of the position of the ROI. How can I visualize it to be sure that the seed of my FS-FAST analysis is effectively the my ROI_MASK? I hope in your help. Thanks in advanced. Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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.
