I'm at a loss here. I run the exact same command with the same version. I get the same terminal output, but my output volume looks ok. The only thing I can think of is that there is an old version that output volume that is not getting overwritten. Can you name the output file differently and make sure that it does not exist prior to running the command?
On 09/30/2015 04:37 PM, Jacobs H (NP) wrote:
Hi Doug,
Just as a reminder: I uploaded the data yesterday.
Best Heidi
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday 29 September 2015 17:01 To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] warping surface label to volume space
filedrop2 url at the end of this email
On 9/29/15 10:34 AM, Jacobs H (NP) wrote:
Sure, where should I upload it to? Thanks! Heidi
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday 29 September 2015 16:28 To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] warping surface label to volume space
Can you upload the subject so I can look at it?
On 9/29/15 9:05 AM, Jacobs H (NP) wrote:
Hi Doug,
The label looks actually ok and the surface as well. I attached the images to this email, Not sure where it went wrong?
Best Heidi
Van:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Douglas N Greve [greve@nmr.mgh.harvard.edu] Verzonden: maandag 28 september 2015 23:58 Aan:freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] warping surface label to volume space
Something is definitely going wrong. Can you load the label as well and verify that the label itself looks ok?
On 09/28/2015 05:32 PM, Jacobs H (NP) wrote:
Yes, here it is! Thanks! Heidi
Yes, here it is! Thanks! Heidi
image1.png
ATT00001.txt
Op 28 sep. 2015 om 17:26 heeft Douglas N Grevegreve@nmr.mgh.harvard.edu het volgende geschreven:
Can you send a picture?
On 09/28/2015 05:08 PM, Jacobs H (NP) wrote: Dear Doug,
By looking at it in Freeview. Anatomically, I would expect that the entorhinal cortex would not be localized so laterally? And some voxels are not in the temporal lobe.
Best Heidi
Van:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Douglas N Greve [greve@nmr.mgh.harvard.edu] Verzonden: maandag 28 september 2015 23:00 Aan:freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] warping surface label to volume space
how are you determining that it is not in the right place? When I run this it works.
> On 09/28/2015 04:54 PM, Jacobs H (NP) wrote: > Hi, > > Bringing this to the FS list: > I am trying to warp the entorhinal cortex label (ex vivo) to volume > space, so that I can see and use the full ROI. Using the command > stated below doesn’t seem to work, as it is not in the right location > of the subject’s brain. Any thoughts? > > I used this command: > mri_label2vol --label S_3RSPPP/label/lh.entorhinal_exvivo.label > --regheader $SUBJECTS_DIR/S_3RSPPP/mri/orig.mgz --o > lh.entorhinal_exvivo_vol.mgz --fill-ribbon --subject S_3RSPPP --hemi l > > This was the output on the terminal: > subject S_3RSPPP --hemi lh > INFO: subject not needed, igorning. > Number of labels: 1 > S_3RSPPP/label/lh.entorhinal_exvivo.label > Annot File: (null) > Template Volume: (null) > Outut Volume: lh.entorhinal_exvivo_vol.mgz > Registration File: (null) > Fill Threshold: 0 > Label Vox Vol: 1 > ProjType: (null) > ProjTypeId: 0 > ProjStart: 0 > ProjStop: 0 > ProjDelta: 0.1 > Subject: S_3RSPPP > Hemi: lh > UseNewASeg2Vol: 0 > DoLabelStatVol 0 > LabelCodeOffset 0 > setenv SUBJECTS_DIR /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS > $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ > INFO: loading > surface /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf/lh.white > > nvertices = 120130 > Reading thickness > /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf/lh.thickness > nlabels = 1 > Loading > /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/mri/ribbon.mgz > Loading S_3RSPPP/label/lh.entorhinal_exvivo.label > Mapping > > Any suggestions how I can improve this? > Thanks > Heidi > > > _______________________________________________ > Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/f... Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/f... Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/f... Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Hi Doug,
Thanks for checking the data! I just removed the output volume, ran the command again and got the same weird output. Since it worked for you, I tried it again… no change. However, then I noticed that the mri_vol2label uses the SUBJECTS_DIR path and this was not set to this folder (I was trying some things out in a temporary folder). So, probably, it was using data from the subject in the original SUBJECTS_DIR folder? I changed that and the output looks beautiful now! It is kind of weird, as the original SUBJECTS_DIR was done in the same version.
But it is working beautifully now!!! Thank you so much for your help! Best Heidi
On 02/10/15 20:57, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
I'm at a loss here. I run the exact same command with the same version. I get the same terminal output, but my output volume looks ok. The only thing I can think of is that there is an old version that output volume that is not getting overwritten. Can you name the output file differently and make sure that it does not exist prior to running the command?
On 09/30/2015 04:37 PM, Jacobs H (NP) wrote:
Hi Doug,
Just as a reminder: I uploaded the data yesterday.
Best Heidi
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday 29 September 2015 17:01 To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] warping surface label to volume space
filedrop2 url at the end of this email
On 9/29/15 10:34 AM, Jacobs H (NP) wrote:
Sure, where should I upload it to? Thanks! Heidi
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday 29 September 2015 16:28 To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] warping surface label to volume space
Can you upload the subject so I can look at it?
On 9/29/15 9:05 AM, Jacobs H (NP) wrote:
Hi Doug,
The label looks actually ok and the surface as well. I attached the images to this email, Not sure where it went wrong?
Best Heidi
Van:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Douglas N Greve [greve@nmr.mgh.harvard.edu] Verzonden: maandag 28 september 2015 23:58 Aan:freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] warping surface label to volume space
Something is definitely going wrong. Can you load the label as well and verify that the label itself looks ok?
On 09/28/2015 05:32 PM, Jacobs H (NP) wrote:
Yes, here it is! Thanks! Heidi
Yes, here it is! Thanks! Heidi
image1.png
ATT00001.txt
Op 28 sep. 2015 om 17:26 heeft Douglas N Grevegreve@nmr.mgh.harvard.edu het volgende geschreven:
Can you send a picture?
> On 09/28/2015 05:08 PM, Jacobs H (NP) wrote: > Dear Doug, > > By looking at it in Freeview. Anatomically, I would expect that >the entorhinal cortex would not be localized so laterally? And some >voxels are not in the temporal lobe. > > Best > Heidi > > ________________________________________ > Van:freesurfer-bounces@nmr.mgh.harvard.edu >[freesurfer-bounces@nmr.mgh.harvard.edu] namens Douglas N Greve >[greve@nmr.mgh.harvard.edu] > Verzonden: maandag 28 september 2015 23:00 > Aan:freesurfer@nmr.mgh.harvard.edu > Onderwerp: Re: [Freesurfer] warping surface label to volume space > > how are you determining that it is not in the right place? When I >run > this it works. > >> On 09/28/2015 04:54 PM, Jacobs H (NP) wrote: >> Hi, >> >> Bringing this to the FS list: >> I am trying to warp the entorhinal cortex label (ex vivo) to >>volume >> space, so that I can see and use the full ROI. Using the command >> stated below doesn’t seem to work, as it is not in the right >>location >> of the subject’s brain. Any thoughts? >> >> I used this command: >> mri_label2vol --label S_3RSPPP/label/lh.entorhinal_exvivo.label >> --regheader $SUBJECTS_DIR/S_3RSPPP/mri/orig.mgz --o >> lh.entorhinal_exvivo_vol.mgz --fill-ribbon --subject S_3RSPPP >>--hemi l >> >> This was the output on the terminal: >> subject S_3RSPPP --hemi lh >> INFO: subject not needed, igorning. >> Number of labels: 1 >> S_3RSPPP/label/lh.entorhinal_exvivo.label >> Annot File: (null) >> Template Volume: (null) >> Outut Volume: lh.entorhinal_exvivo_vol.mgz >> Registration File: (null) >> Fill Threshold: 0 >> Label Vox Vol: 1 >> ProjType: (null) >> ProjTypeId: 0 >> ProjStart: 0 >> ProjStop: 0 >> ProjDelta: 0.1 >> Subject: S_3RSPPP >> Hemi: lh >> UseNewASeg2Vol: 0 >> DoLabelStatVol 0 >> LabelCodeOffset 0 >> setenv SUBJECTS_DIR >>/autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS >> $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ >> INFO: loading >> surface >>/autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf >>/lh.white >> >> nvertices = 120130 >> Reading thickness >> >>/autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf >>/lh.thickness >> nlabels = 1 >> Loading >> >>/autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/mri/ >>ribbon.mgz >> Loading S_3RSPPP/label/lh.entorhinal_exvivo.label >> Mapping >> >> Any suggestions how I can improve this? >> Thanks >> Heidi >> >> >> _______________________________________________ >> Freesurfer mailing list >> >>Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mail >>man/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harva >rd.edu/facility/filedrop/index.html > >Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >ve/ > > _______________________________________________ > Freesurfer mailing list > >Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailm >an/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.eduhttps://mail.nmr.mgh.harvard.edu/mailm
>an/listinfo/freesurfer
Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvar d.edu/facility/filedrop/index.html
Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailma n/listinfo/freesurfer
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman /listinfo/freesurfer _______________________________________________ Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman /listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard. edu/facility/filedrop/index.html
Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Freesurfer mailing list
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Jacobs H (NP)