External Email - Use Caution
Dear Freesurfer experts,
I want to create a new standard template from my study population. For this, I thought about using make_average_subject. Thus, I run: make_average_subject --out avgsubject --subjects REMY001 REMY002 REMY003
I get an error message - ERROR: make_average_surface. Please find attached the error.log.
Would be very thankful for advice!
Many thanks!
/Ben
External Email - Use Caution
As addendum to my message. The full terminal output:
Reading surface
/Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/REMY001_M0//surf/lh.white
Loading annotations from /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/REMY001_M0//label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
CTABwriteFileASCII(/Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.ctab): could not open for writing
No such file or directory
Seg base 0
mghWrite(/Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.mgh, -1): could not open file
Converting to a segmentation
mri_surf2surf --mapmethod nnf --hemi lh --srcsubject REMY001_M0/ --srcsurfreg sphere.reg --sval /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.mgh --trgsubject avgsubject --trgsurfreg sphere.reg --tval /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.std.mgh
mghRead(/Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.mgh, -1): could not open file
Source registration surface changed to sphere.reg
Target registration surface changed to sphere.reg
$Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $
setenv SUBJECTS_DIR /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output
cd /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject
mri_surf2surf --mapmethod nnf --hemi lh --srcsubject REMY001_M0/ --srcsurfreg sphere.reg --sval /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.mgh --trgsubject avgsubject --trgsurfreg sphere.reg --tval /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.std.mgh
sysname Darwin
hostname K8WSBENINE
machine x86_64
user benine
srcsubject = REMY001_M0/
srcval = /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.mgh
srctype =
trgsubject = avgsubject
trgval = /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.std.mgh
trgtype =
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi = lh
trghemi = lh
frame = 0
fwhm-in = 0
fwhm-out = 0
label-src = (null)
label-trg = (null)
OKToRevFaceOrder = 1
UseDualHemi = 0
Reading source surface reg /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/REMY001_M0//surf/lh.sphere.reg
Loading source data
ERROR: could not read /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.mgh as type 3
ERROR: make_average_surface
Thanks!
Am Mi., 26. Feb. 2020 um 10:34 Uhr schrieb Benjamin Ineichen < bv.ineichen@gmail.com>:
Dear Freesurfer experts,
I want to create a new standard template from my study population. For this, I thought about using make_average_subject. Thus, I run: make_average_subject --out avgsubject --subjects REMY001 REMY002 REMY003
I get an error message - ERROR: make_average_surface. Please find attached the error.log.
Would be very thankful for advice!
Many thanks!
/Ben
-- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch +41 76 391 04 01
Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch +41 76 391 04 01
Look at the release notes for how to resolve this http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
On 2/26/2020 4:34 AM, Benjamin Ineichen wrote:
External Email - Use Caution
Dear Freesurfer experts,
I want to create a new standard template from my study population. For this, I thought about using make_average_subject. Thus, I run: make_average_subject --out avgsubject --subjects REMY001 REMY002 REMY003
I get an error message - ERROR: make_average_surface. Please find attached the error.log.
Would be very thankful for advice!
Many thanks!
/Ben
-- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch mailto:ineichen@protonmail.ch +41 76 391 04 01
Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch mailto:ineichen@protonmail.ch +41 76 391 04 01
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Ok. It says that for mac, I need to download the dev release, I assume that refers to Freesurfer version 7.0?
Am Fr., 28. Feb. 2020 um 22:15 Uhr schrieb Douglas N. Greve < dgreve@mgh.harvard.edu>:
Look at the release notes for how to resolve this http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
On 2/26/2020 4:34 AM, Benjamin Ineichen wrote:
External Email - Use CautionDear Freesurfer experts,
I want to create a new standard template from my study population. For this, I thought about using make_average_subject. Thus, I run: make_average_subject --out avgsubject --subjects REMY001 REMY002 REMY003
I get an error message - ERROR: make_average_surface. Please find attached the error.log.
Would be very thankful for advice!
Many thanks!
/Ben
-- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch +41 76 391 04 01
Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch +41 76 391 04 01
Freesurfer mailing listFreesurfer@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
External Email - Use Caution
Respected
want to do a Structural based analysis which constitutes of volume and area, can i correlate or make relation of tracks with same subject.
regards
On Sat, 29 Feb 2020, 20:56 Benjamin Ineichen, bv.ineichen@gmail.com wrote:
External Email - Use CautionOk. It says that for mac, I need to download the dev release, I assume that refers to Freesurfer version 7.0?
Am Fr., 28. Feb. 2020 um 22:15 Uhr schrieb Douglas N. Greve < dgreve@mgh.harvard.edu>:
Look at the release notes for how to resolve this http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
On 2/26/2020 4:34 AM, Benjamin Ineichen wrote:
External Email - Use CautionDear Freesurfer experts,
I want to create a new standard template from my study population. For this, I thought about using make_average_subject. Thus, I run: make_average_subject --out avgsubject --subjects REMY001 REMY002 REMY003
I get an error message - ERROR: make_average_surface. Please find attached the error.log.
Would be very thankful for advice!
Many thanks!
/Ben
-- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch +41 76 391 04 01
Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch +41 76 391 04 01
Freesurfer mailing listFreesurfer@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
-- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch +41 76 391 04 01
Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch +41 76 391 04 01 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
dev or 7beta
On 2/29/2020 10:24 AM, Benjamin Ineichen wrote:
External Email - Use Caution
Ok. It says that for mac, I need to download the dev release, I assume that refers to Freesurfer version 7.0?
Am Fr., 28. Feb. 2020 um 22:15 Uhr schrieb Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>:
Look at the release notes for how to resolve this http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes On 2/26/2020 4:34 AM, Benjamin Ineichen wrote:External Email - Use Caution Dear Freesurfer experts, I want to create a new standard template from my study population. For this, I thought about using make_average_subject. Thus, I run: make_average_subject --out avgsubject --subjects REMY001 REMY002 REMY003 I get an error message - ERROR: make_average_surface. Please find attached the error.log. Would be very thankful for advice! Many thanks! /Ben -- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch <mailto:ineichen@protonmail.ch> +41 76 391 04 01 Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch <mailto:ineichen@protonmail.ch> +41 76 391 04 01 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch mailto:ineichen@protonmail.ch +41 76 391 04 01
Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch mailto:ineichen@protonmail.ch +41 76 391 04 01
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Amar Shukla -
Benjamin Ineichen -
Douglas N. Greve