Re: [Freesurfer] wm parcellation freesurfer
Hi Owais do you mean the wmparc.mgz or the aparc+aseg.mgz? You can use mris_divide_parcellation or mris_make_face_parcellation to subdivide or make an isotropic finer scale one if you want. I believe that you can then create a new aparc+aseg from one of those and then the wmparc from that to get a finer one cheers Bruce On Tue, 28 Jul 2015, Owais Syed wrote: Hi, Is it possible to increase the number of parcellations when making the aparc+aseg file? I have a high resolution MRI, and one parcellation will match every three slides, but I want a better match overall. Thanks, Owais ___ 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] FreeSurfer 6.0 dev version Output
Worked! Thank you so much. Really appreciate the prompt response.
Best,
Priyanka
On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
Cheers,
/E
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: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 11:26:04 AM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Thanks Eugenio! Thats worked!
One more question- how would I convert the lh.CA1.mgz that I get from the
previous step to .nii format?
Best,
Priyanka
On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are interested
in CA1 (label 206), you can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
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: Priyanka priyankamehta0...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the
6.0 dev version.
I used the following command: recon-all -i ${subject}.nii -subject
${subject} -all -hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command:
freeview -v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
However, is there a way I can get a separate .nii file for each of my
hippocampal subregion?
I would really appreciate any help in the matter.
Best,
Priyanka Mehta
___
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Re: [Freesurfer] recon-all -white does not respect wm edits
Dear Bruce, no, both ?h.orig.nofix and ?h.orig are ok (respecting my wm.mgz edits), but only ?h.white (result of mris_make_surfaces) is not ok (leaking to regions where wm.mgz has value 1). Regards, Antonin Hi Antonin if it is correct in the orig.nofix but not correct in the orig that means it was an incorrectly fixed topological defect that you need to manually correct. I'll see if we can find someone here to take a look. Bruce On Wed, 29 Jul 2015, Antonin Skoch wrote: Dear experts, during the manual correction of freesurfer reconstruction I encountered following problem: White surface did not follow gray / white matter boundary probably partly due to skullstrip error and partly to the insufficient local gray/white matter contrast. I tried to fix it by editing wm.mgz, in some cases it worked well, but in some cases white surface does not respect my wm.mgz editing and still leaks out to the areas where wm.mgz has value 1. The problem is probably at the level of recon-all -white since orig.nofix.mgz and orig.mgz are OK - does well follow my edits and does not leak to areas with wm.mgz = 1. I tried to put some control points to these areas but it still did not help (the brainmask.mgz at most of the problematic areas has intensity 110). Processing the data by development version did not help either.? I have uploaded 2 examples to your ftp file exchange: not_corrected_wm_1 - slice 96 in coronal view, right hemisphere, at the convexity - slices 97-98, 103, 107,108, in coronal view,? left hemisphere, at the convexity not_corrected_wm_2 - slices 78 in coronal view, right hemisphere, 2 areas at the convexity - slices 79-83 in coronal view, two quite large areas in both hemispheres at the convexity - slices 88-95 in coronal view, quite large areas at righ hemispheres at the convexity and other areas in following slices, there are quite large amount of them in this subject. Could you please look at the data to find where could be the problem? Thank you very much for all your help. Best regards, Antonin Skoch ___ 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] FreeSurfer 6.0 dev version Output
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
Cheers,
/E
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: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 11:26:04 AM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Thanks Eugenio! Thats worked!
One more question- how would I convert the lh.CA1.mgz that I get from the
previous step to .nii format?
Best,
Priyanka
On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias e.igles...@bcbl.eu wrote:
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are interested in
CA1 (label 206), you can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
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: Priyanka priyankamehta0...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the 6.0
dev version.
I used the following command: recon-all -i ${subject}.nii -subject ${subject}
-all -hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command: freeview
-v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
However, is there a way I can get a separate .nii file for each of my
hippocampal subregion?
I would really appreciate any help in the matter.
Best,
Priyanka Mehta
___
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Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Thanks Eugenio! Thats worked!
One more question- how would I convert the lh.CA1.mgz that I get from the
previous step to .nii format?
Best,
Priyanka
On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are interested
in CA1 (label 206), you can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
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: Priyanka priyankamehta0...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the
6.0 dev version.
I used the following command: recon-all -i ${subject}.nii -subject
${subject} -all -hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command:
freeview -v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
However, is there a way I can get a separate .nii file for each of my
hippocampal subregion?
I would really appreciate any help in the matter.
Best,
Priyanka Mehta
___
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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
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but does not contain patient information, please contact the sender and
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dispose of the e-mail.
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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
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[Freesurfer] randmoness flag and aseg.stats measures
Hello, Similar to the thread below we ran several subjects through the freesurfer (v5.3.0) using the -randomess flag and noticed no differences in the volumes in aseg.stats across the runs. Is this by design? This thread ended here. Pernille, Can you send me the recon-all.log file of one of the subjects? Nick On Fri, 2009-08-21 at 15:19 +0200, Pernille Iversen wrote: * Dear Nick, ** I have now used version 4.5.0 and the -randomness flag no longer gives ** errors, however, after 10 parallel runs of a subject with the ** -randomness flag set, I observe that the stats are completely ** identical. In the logs I can see that the line setting seed for ** random number generator to 1234 is no longer there. In the earlier ** versions where the random initialisation was default I observed ** differences in the stats when I made the 10 parallel runs on the same ** subject as I have used this time - so it would seem that the random ** initialisation is not turned on when I use the flag. Can you please ** comment on this :) * * Thanks, ** Pernille* I also came across this thread separately which seems to indicate that the -randomness flag only changes the cortical measures (which were different across runs for the subjects): Hi Andreia, Then I would guess that your error comes from the fact that you didn't rerun the autorecon3 at that stage for these 2 subjects. *As the randomness flag changes the number of vertices when recreating the surfaces*, that explains the error. I'd appreciate any clarification. Thanks, Keith -- Keith Harenski Mobile MRI Manager Mobile MRI Core and Clinical Cognitive Neuroscience Laboratory The Mind Research Network 1101 Yale Blvd NE Albuquerque, NM 87106-4188 Office: 505.504.1338 | Fax: 505.272.8002 kharen...@mrn.org | www.mrn.org | www.lrri.org ___ 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] Increasing thickness threshold?
Hi FreeSurfer community, I would like to see if FreeSurfer could be used to improve clinical detection of cortical dysplasia. Given that dysplasias can be several mm thicker than typical cortex, are there ways to increase the thickness thresholds to improve detection of cortex that may be up to 10mm thick? Is it possible to increase the thickness measurements beyond 5mm? freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Thank you, Jesse ___ 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] Increasing thickness threshold?
yes, specify -max something biggger than 5 on the command line to mris_thickness and mris_make_surfaces (you can do this in recon-all with expert options) cheers Bruce On Wed, 29 Jul 2015, Jesse Bledsoe wrote: Hi FreeSurfer community, I would like to see if FreeSurfer could be used to improve clinical detection of cortical dysplasia. Given that dysplasias can be several mm thicker than typical cortex, are there ways to increase the thickness thresholds to improve detection of cortex that may be up to 10mm thick? Is it possible to increase the thickness measurements beyond 5mm? freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Thank you, Jesse ___ 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] Pial surface in dural sinus in Longitudinal processing
Hi, Sorry if this is basic- I'm a bit of a novice. I'm running the longitudinal pipeline on patients with three time points. For one of the time points the .long pail surface has included some of the superior sagital sinus as it ascends between the occipital hemispheres. The white matter mask is good, the base image pial surface is good, and the original cross image for this time point also doesn't have this artefact. Reading the longitudinal edits on the wiki it seems to advice agains editing the .long brainmask -even though I think it would resolve this situation if this was in a cross image/subject? I wondered about editing the brain.finalsurfs.mgz image? but the wiki is quite specific about this only being for cerebellar problems. The occipital lobes are are a region of interest in my study so keen to get accurate surfaces. Could you advise on where to go from here to edit this? I hope the above makes sense and thanks for your help! Cheers Justin Dr Justin McKee Clinical Research Fellow in Multiple Sclerosis, Nuffield Department of Clinical Neurosciences, University of Oxford ___ 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] recon-all -white does not respect wm edits
Dear experts, during the manual correction of freesurfer reconstruction I encountered following problem: White surface did not follow gray / white matter boundary probably partly due to skullstrip error and partly to the insufficient local gray/white matter contrast. I tried to fix it by editing wm.mgz, in some cases it worked well, but in some cases white surface does not respect my wm.mgz editing and still leaks out to the areas where wm.mgz has value 1. The problem is probably at the level of recon-all -white since orig.nofix.mgz and orig.mgz are OK - does well follow my edits and does not leak to areas with wm.mgz = 1. I tried to put some control points to these areas but it still did not help (the brainmask.mgz at most of the problematic areas has intensity 110). Processing the data by development version did not help either. I have uploaded 2 examples to your ftp file exchange: not_corrected_wm_1 - slice 96 in coronal view, right hemisphere, at the convexity - slices 97-98, 103, 107,108, in coronal view, left hemisphere, at the convexity not_corrected_wm_2 - slices 78 in coronal view, right hemisphere, 2 areas at the convexity - slices 79-83 in coronal view, two quite large areas in both hemispheres at the convexity - slices 88-95 in coronal view, quite large areas at righ hemispheres at the convexity and other areas in following slices, there are quite large amount of them in this subject. Could you please look at the data to find where could be the problem? Thank you very much for all your help. Best regards, Antonin Skoch___ 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] FreeSurfer 6.0 dev version Output
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are interested in
CA1 (label 206), you can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
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: Priyanka priyankamehta0...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the 6.0
dev version.
I used the following command: recon-all -i ${subject}.nii -subject ${subject}
-all -hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command: freeview
-v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
However, is there a way I can get a separate .nii file for each of my
hippocampal subregion?
I would really appreciate any help in the matter.
Best,
Priyanka Mehta
___
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Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is
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http://www.partners.org/complianceline . If the e-mail was sent to you in error
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[Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the 6.0
dev version.
I used the following command: recon-all -i ${subject}.nii -subject ${subject}
-all -hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command: freeview
-v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
However, is there a way I can get a separate .nii file for each of my
hippocampal subregion?
I would really appreciate any help in the matter.
Best,
Priyanka Mehta
___
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Re: [Freesurfer] FLAIR normalization error
Dear Bruce, I have tested the V6 beta version and the bug with FLAIR normalization seems to be corrected there. Can I patch my 5.3 version to include this bug fix? I suppose V6 beta has many modifications making results from 5.3 and V6 versions incompatible. However, a new problem in V6 beta appeared: it seems that mris_make_surfaces in V6 beta ignores nsigma_above option. The gray matter regions after FLAIRpial refinement are cut out in high intensity FLAIR areas. Modifying nsigma_above (which helped in 5.3. version) does not have an effect in V6 beta. There is a new entry in log file (not present in 5.3 version): resetting max gray (value depending on set nsigma_above) based on CDF to 168 which supposedly overrides my nsigma_above modification. I have uploaded the subject (FLAIRnorm_not_OK_nsigma_above_8.tar.gz) to your server if you would like to take a look. Regards, Antonin Skoch _ hmmm, that could be a problem, although the surfaces look pretty good, so maybe not. Try V6 beta and see if it still happens. Or upload the subject and we will try it out cheers Bruce On Fri, 19 Jun 2015, Antonin Skoch wrote: Dear FreeSurfer experts, I encountered possible bug in FLAIR intensity normalization in several subjects. See attached screenshots with FLAIR.prenorm.mgz and FLAIR.mgz files. The normal intensity pixels in FLAIR.mgz have intensity around 100, whereas bright pixels (see FLAIR_after_normalization2.png file) have intensities above 1000. There are several pixels outside head (seen in FLAIR_normalization2.png file) with value 32767. Regards, Antonin Skoch ___ 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] dev version of mri_ca_label memory leak?
Ok how can I send you the files and commands? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, 30 July 2015 12:03 AM To: Freesurfer support list Subject: Re: [Freesurfer] dev version of mri_ca_label memory leak? Hi Chris if you send me all the inputs to mri_ca_label and your exact command line I'll see if I can replicate it and either fix it or send you a new version. Or you can try the current dev version and see if it fixes things cheers Bruce On Wed, 29 Jul 2015, Chris Adamson wrote: Devs, I’m running the CVS version of Freesurfer, checked out on 28/7/2015 (7/28/2015 for US people). I get to the –calabel step and mri_ca_label takes a *long* time (400 minutes) and uses a *lot* of memory. After it outputs “saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt” the memory consumption continues to increase. Currently it is at 8.9GB. Can I send output to help debug this? Chris. Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children’s Hospital Flemington Road, Parkville, Victoria 3052, Australia www.mcri.edu.au E chris.adam...@mcri.edu.au T 03 9936 6780 __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com __ __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com If you have any questions, please contact MCRI IT Servicedesk for further assistance. __ __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com __ ___ 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] extracting subcortical volumes from longitudinal processed data
Hi all, I am trying to extract subcortical volumes from data that has been processed longitudinally, but I am getting the following error. [k1204763@nanlnx9 SAGA]0% asegstats2table --qdec-long long.qdec.table.dat --stats aseg.stats --tablefile aseg.table.txt SUBJECTS_DIR : /home/k1204763/images/SAGA Traceback (most recent call last): File /software/system/freesurfer/freesurfer-5.3.0/bin/asegstats2table, line 514, in module subj_listoftuples = assemble_inputs(options) File /software/system/freesurfer/freesurfer-5.3.0/bin/asegstats2table, line 323, in assemble_inputs o.subjects.append(fsid+'.long.'+row['fsid-base'].strip()) KeyError: 'fsid-base' Do you have any ideas as to what the issue is here? Thanks, Amanda ___ 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] recon-all -white does not respect wm edits
Hi Antonin if it is correct in the orig.nofix but not correct in the orig that means it was an incorrectly fixed topological defect that you need to manually correct. I'll see if we can find someone here to take a look. Bruce On Wed, 29 Jul 2015, Antonin Skoch wrote: Dear experts, during the manual correction of freesurfer reconstruction I encountered following problem: White surface did not follow gray / white matter boundary probably partly due to skullstrip error and partly to the insufficient local gray/white matter contrast. I tried to fix it by editing wm.mgz, in some cases it worked well, but in some cases white surface does not respect my wm.mgz editing and still leaks out to the areas where wm.mgz has value 1. The problem is probably at the level of recon-all -white since orig.nofix.mgz and orig.mgz are OK - does well follow my edits and does not leak to areas with wm.mgz = 1. I tried to put some control points to these areas but it still did not help (the brainmask.mgz at most of the problematic areas has intensity 110). Processing the data by development version did not help either. I have uploaded 2 examples to your ftp file exchange: not_corrected_wm_1 - slice 96 in coronal view, right hemisphere, at the convexity - slices 97-98, 103, 107,108, in coronal view, left hemisphere, at the convexity not_corrected_wm_2 - slices 78 in coronal view, right hemisphere, 2 areas at the convexity - slices 79-83 in coronal view, two quite large areas in both hemispheres at the convexity - slices 88-95 in coronal view, quite large areas at righ hemispheres at the convexity and other areas in following slices, there are quite large amount of them in this subject. Could you please look at the data to find where could be the problem? Thank you very much for all your help. Best regards, Antonin Skoch ___ 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] dev version of mri_ca_label memory leak?
Hi Chris if you send me all the inputs to mri_ca_label and your exact command line I'll see if I can replicate it and either fix it or send you a new version. Or you can try the current dev version and see if it fixes things cheers Bruce On Wed, 29 Jul 2015, Chris Adamson wrote: Devs, I’m running the CVS version of Freesurfer, checked out on 28/7/2015 (7/28/2015 for US people). I get to the –calabel step and mri_ca_label takes a *long* time (400 minutes) and uses a *lot* of memory. After it outputs “saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt” the memory consumption continues to increase. Currently it is at 8.9GB. Can I send output to help debug this? Chris. Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children’s Hospital Flemington Road, Parkville, Victoria 3052, Australia www.mcri.edu.au E chris.adam...@mcri.edu.au T 03 9936 6780 __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com __ ___ 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.
