Dear FreeSurfer experts,
I ran mri-glmfit-sim using mc-z, for both hemispheres, and the right hemi finished with the message “mri_glmfit-sim done”.
However, for the left hemi, I got the following: “ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!”
I believe this is signifying that there were no clusters that survived the correction, but would like to verify with you guys.
Thank you so much.
Best,
Fred
Can you send the command line and full terminal output?
On 02/16/2017 12:54 PM, Uquillas, Federico D'Oleire wrote:
Dear FreeSurfer experts,
I ran mri-glmfit-sim using mc-z, for both hemispheres, and the right hemi finished with the message “mri_glmfit-sim done”.
However, for the left hemi, I got the following: “ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!”
I believe this is signifying that there were no clusters that survived the correction, but would like to verify with you guys.
Thank you so much.
Best,
Fred
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
The command line was the following (its simply a copy of the right side hemi command though, which ran successfully with no errors.): mri_glmfit-sim --glmdir lh.N47_edited_BL_CT_PiB_centAge_fsgd.doss.15.glmdir/ --sim mc-z 1000 1.3 mc-z.abs.13 --sim-sign abs
Is there a way for me to send you the terminal output that's not via email. The txt file where I copied it to is 36MB and I also can't seem to be able to copy and paste it to this email. It's basically this over and over again thousands of times: MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842
and the final line of the output is: ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!
Thank you Doug.
Best,
Fred
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, February 16, 2017 1:30 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] “ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!"
Can you send the command line and full terminal output?
On 02/16/2017 12:54 PM, Uquillas, Federico D'Oleire wrote:
Dear FreeSurfer experts,
I ran mri-glmfit-sim using mc-z, for both hemispheres, and the right hemi finished with the message “mri_glmfit-sim done”.
However, for the left hemi, I got the following: “ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!”
I believe this is signifying that there were no clusters that survived the correction, but would like to verify with you guys.
Thank you so much.
Best,
Fred
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/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Can you tar up the glmdir and send it to me on our file drop (see url below)?
On 02/16/2017 02:01 PM, Uquillas, Federico D'Oleire wrote:
Hi Doug,
The command line was the following (its simply a copy of the right side hemi command though, which ran successfully with no errors.): mri_glmfit-sim --glmdir lh.N47_edited_BL_CT_PiB_centAge_fsgd.doss.15.glmdir/ --sim mc-z 1000 1.3 mc-z.abs.13 --sim-sign abs
Is there a way for me to send you the terminal output that's not via email. The txt file where I copied it to is 36MB and I also can't seem to be able to copy and paste it to this email. It's basically this over and over again thousands of times: MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842
and the final line of the output is: ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!
Thank you Doug.
Best,
Fred
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, February 16, 2017 1:30 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] “ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!"
Can you send the command line and full terminal output?
On 02/16/2017 12:54 PM, Uquillas, Federico D'Oleire wrote:
Dear FreeSurfer experts,
I ran mri-glmfit-sim using mc-z, for both hemispheres, and the right hemi finished with the message “mri_glmfit-sim done”.
However, for the left hemi, I got the following: “ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!”
I believe this is signifying that there were no clusters that survived the correction, but would like to verify with you guys.
Thank you so much.
Best,
Fred
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/
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
Thanks Doug. I did just now.
Best,
Fred
On 2/16/17, 2:05 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:
Can you tar up the glmdir and send it to me on our file drop (see url below)?
On 02/16/2017 02:01 PM, Uquillas, Federico D'Oleire wrote:
Hi Doug,
The command line was the following (its simply a copy of the right side hemi command though, which ran successfully with no errors.): mri_glmfit-sim --glmdir lh.N47_edited_BL_CT_PiB_centAge_fsgd.doss.15.glmdir/ --sim mc-z 1000 1.3 mc-z.abs.13 --sim-sign abs
Is there a way for me to send you the terminal output that's not via email. The txt file where I copied it to is 36MB and I also can't seem to be able to copy and paste it to this email. It's basically this over and over again thousands of times: MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842
and the final line of the output is: ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!
Thank you Doug.
Best,
Fred
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, February 16, 2017 1:30 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] “ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!"
Can you send the command line and full terminal output?
On 02/16/2017 12:54 PM, Uquillas, Federico D'Oleire wrote:
Dear FreeSurfer experts,
I ran mri-glmfit-sim using mc-z, for both hemispheres, and the right hemi finished with the message “mri_glmfit-sim done”.
However, for the left hemi, I got the following: “ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!”
I believe this is signifying that there were no clusters that survived the correction, but would like to verify with you guys.
Thank you so much.
Best,
Fred
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/
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
-- 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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry for the delay. I could not replicate this error on my end. It looks like the $FREESURFER_HOME/subjects/fsaverage/label/lh.aparc.annot might be bad on your system. Try this
tksurfer fsaverage lh inflated -aparc
does that generate the same errors?
On 02/16/2017 02:35 PM, Uquillas, Federico D'Oleire wrote:
Thanks Doug. I did just now.
Best,
Fred
On 2/16/17, 2:05 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:
Can you tar up the glmdir and send it to me on our file drop (see url below)?
On 02/16/2017 02:01 PM, Uquillas, Federico D'Oleire wrote:
Hi Doug,
The command line was the following (its simply a copy of the right side hemi command though, which ran successfully with no errors.): mri_glmfit-sim --glmdir lh.N47_edited_BL_CT_PiB_centAge_fsgd.doss.15.glmdir/ --sim mc-z 1000 1.3 mc-z.abs.13 --sim-sign abs
Is there a way for me to send you the terminal output that's not via email. The txt file where I copied it to is 36MB and I also can't seem to be able to copy and paste it to this email. It's basically this over and over again thousands of times: MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842
and the final line of the output is: ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!
Thank you Doug.
Best,
Fred
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, February 16, 2017 1:30 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] “ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!"
Can you send the command line and full terminal output?
On 02/16/2017 12:54 PM, Uquillas, Federico D'Oleire wrote:
Dear FreeSurfer experts,
I ran mri-glmfit-sim using mc-z, for both hemispheres, and the right hemi finished with the message “mri_glmfit-sim done”.
However, for the left hemi, I got the following: “ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!”
I believe this is signifying that there were no clusters that survived the correction, but would like to verify with you guys.
Thank you so much.
Best,
Fred
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/
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
-- 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/
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
Hi Doug, thanks so much for looking into this. I just ran that comman and I get the same errors indeed.
Would you be able to recommend a way for us to fix this so we can look at the left hemi significant clusters after mri_glmfit-sim?
Best,
Fred
On 2/21/17, 11:33 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:
Sorry for the delay. I could not replicate this error on my end. It looks like the $FREESURFER_HOME/subjects/fsaverage/label/lh.aparc.annot might be bad on your system. Try this
tksurfer fsaverage lh inflated -aparc
does that generate the same errors?
On 02/16/2017 02:35 PM, Uquillas, Federico D'Oleire wrote:
Thanks Doug. I did just now.
Best,
Fred
On 2/16/17, 2:05 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:
Can you tar up the glmdir and send it to me on our file drop (see url below)?
On 02/16/2017 02:01 PM, Uquillas, Federico D'Oleire wrote:
Hi Doug,
The command line was the following (its simply a copy of the right side hemi command though, which ran successfully with no errors.): mri_glmfit-sim --glmdir lh.N47_edited_BL_CT_PiB_centAge_fsgd.doss.15.glmdir/ --sim mc-z 1000 1.3 mc-z.abs.13 --sim-sign abs
Is there a way for me to send you the terminal output that's not via email. The txt file where I copied it to is 36MB and I also can't seem to be able to copy and paste it to this email. It's basically this over and over again thousands of times: MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842
and the final line of the output is: ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!
Thank you Doug.
Best,
Fred
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, February 16, 2017 1:30 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] “ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!"
Can you send the command line and full terminal output?
On 02/16/2017 12:54 PM, Uquillas, Federico D'Oleire wrote:
Dear FreeSurfer experts,
I ran mri-glmfit-sim using mc-z, for both hemispheres, and the right hemi finished with the message “mri_glmfit-sim done”.
However, for the left hemi, I got the following: “ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!”
I believe this is signifying that there were no clusters that survived the correction, but would like to verify with you guys.
Thank you so much.
Best,
Fred
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/
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
-- 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/
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
-- 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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I think your installation of FS got corrupted. Try downloading and reinstalling FS (same version of what you have). If you want, you can just copy over fsaverage from the new download.
On 02/21/2017 11:50 AM, Uquillas, Federico D'Oleire wrote:
Hi Doug, thanks so much for looking into this. I just ran that comman and I get the same errors indeed.
Would you be able to recommend a way for us to fix this so we can look at the left hemi significant clusters after mri_glmfit-sim?
Best,
Fred
On 2/21/17, 11:33 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:
Sorry for the delay. I could not replicate this error on my end. It looks like the $FREESURFER_HOME/subjects/fsaverage/label/lh.aparc.annot might be bad on your system. Try this
tksurfer fsaverage lh inflated -aparc
does that generate the same errors?
On 02/16/2017 02:35 PM, Uquillas, Federico D'Oleire wrote:
Thanks Doug. I did just now.
Best,
Fred
On 2/16/17, 2:05 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:
Can you tar up the glmdir and send it to me on our file drop (see url below)?
On 02/16/2017 02:01 PM, Uquillas, Federico D'Oleire wrote:
Hi Doug,
The command line was the following (its simply a copy of the right side hemi command though, which ran successfully with no errors.): mri_glmfit-sim --glmdir lh.N47_edited_BL_CT_PiB_centAge_fsgd.doss.15.glmdir/ --sim mc-z 1000 1.3 mc-z.abs.13 --sim-sign abs
Is there a way for me to send you the terminal output that's not via email. The txt file where I copied it to is 36MB and I also can't seem to be able to copy and paste it to this email. It's basically this over and over again thousands of times: MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842 annot file: /autofs/space/rincewind_002/users/PiB_BL-MR/fsaverage/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 134219776 i=08000800, in_array_size=163842
and the final line of the output is: ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!
Thank you Doug.
Best,
Fred
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, February 16, 2017 1:30 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] “ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!"
Can you send the command line and full terminal output?
On 02/16/2017 12:54 PM, Uquillas, Federico D'Oleire wrote:
Dear FreeSurfer experts,
I ran mri-glmfit-sim using mc-z, for both hemispheres, and the right hemi finished with the message “mri_glmfit-sim done”.
However, for the left hemi, I got the following: “ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!”
I believe this is signifying that there were no clusters that survived the correction, but would like to verify with you guys.
Thank you so much.
Best,
Fred
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- 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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Uquillas, Federico D'Oleire