External Email - Use Caution
Hi Freesurfers,
I'm trying to project the surface, a fine-grained parcellation (?h.250.aparc.annot), into volume space (dti_FA) with
for subj in SPN01*; do if [ -d "${subj}" ]; then cd $subj/ mri_surf2vol \ --o FA/annot2FA.nii.gz \ --subject $subj \ --so $SUBJECTS_DIR/$subj/label/lh.250.aparc.annot $dtipath/$subj/dti_FA.nii.gz cd ../ fi done
However, I get ERROR: MRISread: file '$SUBJECTS_DIR/$subj/label/lh.250.aparc.annot' has more faces than vertices! How can I solve this?
Thanks, Stephanie
Stephanie Winkelbeiner, MSc Research Coordinator Psychiatry Research Zucker Hillside Hospital 75-59 263 Street Glen Oaks, NY 11004 Tel: (718) 470-4588 Email: swinkelbei@northwell.edumailto:swinkelbei@northwell.edu
Northwell Health Visit us at Northwell.eduhttp://northwell.edu/
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
Hi Stephanie
the -so switch requirees a surface and an overlay. What you have given it is an annotation (NOT a surface) and an overlay. Use one of the surfaces instead (e.g. lh.white)
cheers Bruce
On Sun, 9 Dec 2018, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Hi Freesurfers,
I’m trying to project the surface, a fine-grained parcellation (?h.250.aparc.annot), into volume space (dti_FA) with
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
mri_surf2vol \
--o FA/annot2FA.nii.gz \
--subject $subj \
--so $SUBJECTS_DIR/$subj/label/lh.250.aparc.annot $dtipath/$subj/dti_FA.nii.gz
cd ../
fi
done
However, I get ERROR: MRISread: file ‘$SUBJECTS_DIR/$subj/label/lh.250.aparc.annot’ has more faces than vertices!
How can I solve this?
Thanks,
Stephanie
Stephanie Winkelbeiner, MSc
Research Coordinator
Psychiatry Research
Zucker Hillside Hospital
75-59 263 Street
Glen Oaks, NY 11004
Tel: (718) 470-4588
Email: swinkelbei@northwell.edu
Northwell Health
Visit us at Northwell.edu
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
External Email - Use Caution
Dear Bruce,
Thanks for your quick and helpful reply!
Using the surface lh.white has worked perfectly.
Do I understand correctly that the output file is the FA volume conform with the lh.white surface? Therefore, if I wanted to extract the mean FA for each parcel I would use this newly created volume and the annotation file? I had previously used mri_segstats, but that wouldn't work here. Is that right?
Cheers, Steph
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Sunday, December 09, 2018 4:48 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
Hi Stephanie
the -so switch requirees a surface and an overlay. What you have given it is an annotation (NOT a surface) and an overlay. Use one of the surfaces instead (e.g. lh.white)
cheers Bruce
On Sun, 9 Dec 2018, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Hi Freesurfers,
I’m trying to project the surface, a fine-grained parcellation (?h.250.aparc.annot), into volume space (dti_FA) with
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
mri_surf2vol \
--o FA/annot2FA.nii.gz \
--subject $subj \
--so $SUBJECTS_DIR/$subj/label/lh.250.aparc.annot $dtipath/$subj/dti_FA.nii.gz
cd ../
fi
done
However, I get ERROR: MRISread: file ‘$SUBJECTS_DIR/$subj/label/lh.250.aparc.annot’ has more faces than vertices!
How can I solve this?
Thanks,
Stephanie
Stephanie Winkelbeiner, MSc
Research Coordinator
Psychiatry Research
Zucker Hillside Hospital
75-59 263 Street
Glen Oaks, NY 11004
Tel: (718) 470-4588
Email: swinkelbei@northwell.edu
Northwell Health
Visit us at Northwell.edu
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
Hi Steph
I think that mri_segstats would work, but I defer to Doug. The output should be normal volume, viewable in freeview. I'm not sure why you would want to do this with FA though. Maybe you could give us more details about what you are trying to accomplish? Seems like you want to project the annot into the volume, not the FA maps. Not sure if surf2vol takes annots, again Doug would know
cheers. Bruce On Sun, 9 Dec 2018, Winkelbeiner, Stephanie A wrote:
External Email - Use CautionDear Bruce,
Thanks for your quick and helpful reply!
Using the surface lh.white has worked perfectly.
Do I understand correctly that the output file is the FA volume conform with the lh.white surface? Therefore, if I wanted to extract the mean FA for each parcel I would use this newly created volume and the annotation file? I had previously used mri_segstats, but that wouldn't work here. Is that right?
Cheers, Steph
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Sunday, December 09, 2018 4:48 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
Hi Stephanie
the -so switch requirees a surface and an overlay. What you have given it is an annotation (NOT a surface) and an overlay. Use one of the surfaces instead (e.g. lh.white)
cheers Bruce
On Sun, 9 Dec 2018, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Hi Freesurfers,
I’m trying to project the surface, a fine-grained parcellation (?h.250.aparc.annot), into volume space (dti_FA) with
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
mri_surf2vol \
--o FA/annot2FA.nii.gz \
--subject $subj \
--so $SUBJECTS_DIR/$subj/label/lh.250.aparc.annot $dtipath/$subj/dti_FA.nii.gz
cd ../
fi
done
However, I get ERROR: MRISread: file ‘$SUBJECTS_DIR/$subj/label/lh.250.aparc.annot’ has more faces than vertices!
How can I solve this?
Thanks,
Stephanie
Stephanie Winkelbeiner, MSc
Research Coordinator
Psychiatry Research
Zucker Hillside Hospital
75-59 263 Street
Glen Oaks, NY 11004
Tel: (718) 470-4588
Email: swinkelbei@northwell.edu
Northwell Health
Visit us at Northwell.edu
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Bruce,
you are exactly right. We are interested in projecting the parcellations into the WM to extract the corresponding FA values.
I had tried
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
# extract FA
mri_segstats \
--seg mri/parc2502dwi.nii.gz \ # parcellation extended & registered to dti_FA.nii.gz
--ctab colortable.txt \
--i $dtipath/$subj/dti_FA.nii.gz \
--excludeid 0 \
--sum ../FA/${subj}_fa.stats
cd ../
fi
done
but had so many zero values that I wanted to check first if I get values for all the parcels if I use the non-extended annot-file.
Thanks a lot for helping me with this problem! Cheers, Steph
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Sunday, 9 December 2018 5:24 PM To: Freesurfer support list Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
Hi Steph
I think that mri_segstats would work, but I defer to Doug. The output
should be normal volume, viewable in freeview. I'm not sure why you would
want to do this with FA though. Maybe you could give us more details about
what you are trying to accomplish? Seems like you want to project the annot
into the volume, not the FA maps. Not sure if surf2vol takes annots, again
Doug would know
cheers.
Bruce
On Sun, 9 Dec
2018, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Dear Bruce,
Thanks for your quick and helpful reply!
Using the surface lh.white has worked perfectly.
Do I understand correctly that the output file is the FA volume conform
with the lh.white surface? Therefore, if I wanted to extract the mean FA
for each parcel I would use this newly created volume and the annotation
file? I had previously used mri_segstats, but that wouldn't work here. Is
that right?
Cheers,
Steph
-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Sunday, December 09, 2018 4:48 PM
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Subject: [EXTERNAL] Re: [Freesurfer] mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
Hi Stephanie
the -so switch requirees a surface and an overlay. What you have given it is an annotation (NOT a surface) and an overlay. Use one of the surfaces instead (e.g. lh.white)
cheers
Bruce
On Sun, 9 Dec 2018,
Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Hi Freesurfers,
I’m trying to project the surface, a fine-grained parcellation
(?h.250.aparc.annot), into volume space (dti_FA) with
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
mri_surf2vol \
--o FA/annot2FA.nii.gz \
--subject $subj \
--so $SUBJECTS_DIR/$subj/label/lh.250.aparc.annot
$dtipath/$subj/dti_FA.nii.gz
cd ../
fi
done
However, I get ERROR: MRISread: file
‘$SUBJECTS_DIR/$subj/label/lh.250.aparc.annot’ has more faces than vertices!
How can I solve this?
Thanks,
Stephanie
Stephanie Winkelbeiner, MSc
Research Coordinator
Psychiatry Research
Zucker Hillside Hospital
75-59 263 Street
Glen Oaks, NY 11004
Tel: (718) 470-4588
Email: swinkelbei@northwell.edu
Northwell Health
Visit us at Northwell.edu
The information contained in this electronic e-mail transmission and
any attachments are intended only for the use of the individual or
entity to whom or to which it is addressed, and may contain
information that is privileged, confidential and exempt from
disclosure under applicable law. If the reader of this communication
is not the intended recipient, or the employee or agent responsible
for delivering this communication to the intended recipient, you are
hereby notified that any dissemination, distribution, copying or
disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium.
Receipt by anyone other than the intended recipient is not a waiver of
any attorney-client, physician-patient or other privilege.
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
External Email - Use Caution
Hi Douglas,
I was wondering if I can use an annot file in surf2vol to project those parcels into the FA image space? Or would label2vol be more appropriate? Bruce was so kind to give me his advice already and we discussed my challenges a bit (see below).
Besides surf2vol with lh.white, I tried the following:
for subj in SPN01*; do if [ -d "${subj}" ]; then cd $subj/ mri_label2vol \ --annot label/lh.250.aparc.annot \ --temp $dtipath/$subj/dti_FA.nii.gz \ --reg mri/register.dat \ --proj abs -3 -2 .1 \ --subject $subj --hemi lh \ --o mri/vol250-lh.nii.gz cd ../ fi done
Then, I used the vol250-lh image with mri_segstats to get the FA values (see below). This gives reasonable FA values.
Would you consider this a valid approach?
I'd greatly appreciate your input. Cheers, Steph
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Winkelbeiner, Stephanie A Sent: Sunday, December 09, 2018 8:58 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
External Email - Use Caution
Hi Bruce,
you are exactly right. We are interested in projecting the parcellations into the WM to extract the corresponding FA values.
I had tried
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
# extract FA
mri_segstats \
--seg mri/parc2502dwi.nii.gz \ # parcellation extended & registered to dti_FA.nii.gz
--ctab colortable.txt \
--i $dtipath/$subj/dti_FA.nii.gz \
--excludeid 0 \
--sum ../FA/${subj}_fa.stats
cd ../
fi
done
but had so many zero values that I wanted to check first if I get values for all the parcels if I use the non-extended annot-file.
Thanks a lot for helping me with this problem! Cheers, Steph
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> Sent: Sunday, 9 December 2018 5:24 PM To: Freesurfer support list Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
Hi Steph
I think that mri_segstats would work, but I defer to Doug. The output
should be normal volume, viewable in freeview. I'm not sure why you would
want to do this with FA though. Maybe you could give us more details about
what you are trying to accomplish? Seems like you want to project the annot
into the volume, not the FA maps. Not sure if surf2vol takes annots, again
Doug would know
cheers.
Bruce
On Sun, 9 Dec
2018, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Dear Bruce,
Thanks for your quick and helpful reply!
Using the surface lh.white has worked perfectly.
Do I understand correctly that the output file is the FA volume conform
with the lh.white surface? Therefore, if I wanted to extract the mean FA
for each parcel I would use this newly created volume and the annotation
file? I had previously used mri_segstats, but that wouldn't work here. Is
that right?
Cheers,
Steph
-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Sunday, December 09, 2018 4:48 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [EXTERNAL] Re: [Freesurfer] mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
Hi Stephanie
the -so switch requirees a surface and an overlay. What you have given it is an annotation (NOT a surface) and an overlay. Use one of the surfaces instead (e.g. lh.white)
cheers
Bruce
On Sun, 9 Dec 2018,
Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Hi Freesurfers,
I’m trying to project the surface, a fine-grained parcellation
(?h.250.aparc.annot), into volume space (dti_FA) with
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
mri_surf2vol \
--o FA/annot2FA.nii.gz \
--subject $subj \
--so $SUBJECTS_DIR/$subj/label/lh.250.aparc.annot
$dtipath/$subj/dti_FA.nii.gz
cd ../
fi
done
However, I get ERROR: MRISread: file
‘$SUBJECTS_DIR/$subj/label/lh.250.aparc.annot’ has more faces than vertices!
How can I solve this?
Thanks,
Stephanie
Stephanie Winkelbeiner, MSc
Research Coordinator
Psychiatry Research
Zucker Hillside Hospital
75-59 263 Street
Glen Oaks, NY 11004
Tel: (718) 470-4588
Email: swinkelbei@northwell.edumailto:swinkelbei@northwell.edu
Northwell Health
Visit us at Northwell.edu
The information contained in this electronic e-mail transmission and
any attachments are intended only for the use of the individual or
entity to whom or to which it is addressed, and may contain
information that is privileged, confidential and exempt from
disclosure under applicable law. If the reader of this communication
is not the intended recipient, or the employee or agent responsible
for delivering this communication to the intended recipient, you are
hereby notified that any dissemination, distribution, copying or
disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium.
Receipt by anyone other than the intended recipient is not a waiver of
any attorney-client, physician-patient or other privilege.
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
That all looks like it would work to me. Another thing you can try is the way we create the wmparc.mgz using mri_aparc2aseg. You can find the commandline in the recon-all.log file (make sure to set the output name so that you don't overwrite wmparc.mgz). You can specify the max distance away from cortex that the label can grow.
On 12/10/18 5:06 PM, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution Hi Douglas,
I was wondering if I can use an annot file in surf2vol to project those parcels into the FA image space? Or would label2vol be more appropriate? Bruce was so kind to give me his advice already and we discussed my challenges a bit (see below).
Besides surf2vol with lh.white, I tried the following:
for subj in SPN01*; do if [ -d "${subj}" ]; then cd $subj/ mri_label2vol \ --annot label/lh.250.aparc.annot \ --temp $dtipath/$subj/dti_FA.nii.gz \ --reg mri/register.dat \ --proj abs -3 -2 .1 \ --subject $subj --hemi lh \ --o mri/vol250-lh.nii.gz cd ../ fi done
Then, I used the vol250-lh image with mri_segstats to get the FA values (see below). This gives reasonable FA values.
Would you consider this a valid approach?
I’d greatly appreciate your input. Cheers, Steph
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Winkelbeiner, Stephanie A Sent: Sunday, December 09, 2018 8:58 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
External Email - Use Caution
Hi Bruce,
you are exactly right. We are interested in projecting the parcellations into the WM to extract the corresponding FA values.
I had tried
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
# extract FA
mri_segstats \
--seg mri/parc2502dwi.nii.gz \ # parcellation extended & registered to dti_FA.nii.gz
--ctab colortable.txt \
--i $dtipath/$subj/dti_FA.nii.gz \
--excludeid 0 \
--sum ../FA/${subj}_fa.stats
cd ../
fi
done
but had so many zero values that I wanted to check first if I get values for all the parcels if I use the non-extended annot-file.
Thanks a lot for helping me with this problem! Cheers, Steph
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> Sent: Sunday, 9 December 2018 5:24 PM To: Freesurfer support list Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
Hi Steph
I think that mri_segstats would work, but I defer to Doug. The output
should be normal volume, viewable in freeview. I'm not sure why you would
want to do this with FA though. Maybe you could give us more details about
what you are trying to accomplish? Seems like you want to project the annot
into the volume, not the FA maps. Not sure if surf2vol takes annots, again
Doug would know
cheers.
Bruce
On Sun, 9 Dec
2018, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Dear Bruce,
Thanks for your quick and helpful reply!
Using the surface lh.white has worked perfectly.
Do I understand correctly that the output file is the FA volume conform
with the lh.white surface? Therefore, if I wanted to extract the mean FA
for each parcel I would use this newly created volume and the annotation
file? I had previously used mri_segstats, but that wouldn't work here. Is
that right?
Cheers,
Steph
-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Sunday, December 09, 2018 4:48 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [EXTERNAL] Re: [Freesurfer] mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
Hi Stephanie
the -so switch requirees a surface and an overlay. What you have given it is an annotation (NOT a surface) and an overlay. Use one of the surfaces instead (e.g. lh.white)
cheers
Bruce
On Sun, 9 Dec 2018,
Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Hi Freesurfers,
I’m trying to project the surface, a fine-grained parcellation
(?h.250.aparc.annot), into volume space (dti_FA) with
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
mri_surf2vol \
--o FA/annot2FA.nii.gz \
--subject $subj \
--so $SUBJECTS_DIR/$subj/label/lh.250.aparc.annot
$dtipath/$subj/dti_FA.nii.gz
cd ../
fi
done
However, I get ERROR: MRISread: file
‘$SUBJECTS_DIR/$subj/label/lh.250.aparc.annot’ has more faces than vertices!
How can I solve this?
Thanks,
Stephanie
Stephanie Winkelbeiner, MSc
Research Coordinator
Psychiatry Research
Zucker Hillside Hospital
75-59 263 Street
Glen Oaks, NY 11004
Tel: (718) 470-4588
Email: swinkelbei@northwell.edumailto:swinkelbei@northwell.edu
Northwell Health
Visit us at Northwell.edu
The information contained in this electronic e-mail transmission and
any attachments are intended only for the use of the individual or
entity to whom or to which it is addressed, and may contain
information that is privileged, confidential and exempt from
disclosure under applicable law. If the reader of this communication
is not the intended recipient, or the employee or agent responsible
for delivering this communication to the intended recipient, you are
hereby notified that any dissemination, distribution, copying or
disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium.
Receipt by anyone other than the intended recipient is not a waiver of
any attorney-client, physician-patient or other privilege.
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
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The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Doug,
Thanks a lot for getting back to me and your helpful comments! Good that you mention the mri_aparc2aseg option. I had tried that and registered the resulting volume aparc.250+2mm.nii.gz to DTI space (bbregister and mri_vol2vol). Yet, extracting the FA values (mri_segstats) resulted in >70% of parcels having zero values (with the label2vol approach I get values in almost all parcels). I checked, aparc.250+2mm.nii.gz and dti_FA.nii.gz seem to be perfectly coregistered. Could you think of any reason why that is?
Thanks, Steph
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, December 11, 2018 10:49 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
External Email. Use Caution. That all looks like it would work to me. Another thing you can try is the way we create the wmparc.mgz using mri_aparc2aseg. You can find the commandline in the recon-all.log file (make sure to set the output name so that you don't overwrite wmparc.mgz). You can specify the max distance away from cortex that the label can grow. On 12/10/18 5:06 PM, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution Hi Douglas,
I was wondering if I can use an annot file in surf2vol to project those parcels into the FA image space? Or would label2vol be more appropriate? Bruce was so kind to give me his advice already and we discussed my challenges a bit (see below).
Besides surf2vol with lh.white, I tried the following:
for subj in SPN01*; do if [ -d "${subj}" ]; then cd $subj/ mri_label2vol \ --annot label/lh.250.aparc.annot \ --temp $dtipath/$subj/dti_FA.nii.gz \ --reg mri/register.dat \ --proj abs -3 -2 .1 \ --subject $subj --hemi lh \ --o mri/vol250-lh.nii.gz cd ../ fi done
Then, I used the vol250-lh image with mri_segstats to get the FA values (see below). This gives reasonable FA values.
Would you consider this a valid approach?
I’d greatly appreciate your input. Cheers, Steph
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Winkelbeiner, Stephanie A Sent: Sunday, December 09, 2018 8:58 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
External Email - Use Caution
Hi Bruce,
you are exactly right. We are interested in projecting the parcellations into the WM to extract the corresponding FA values.
I had tried
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
# extract FA
mri_segstats \
--seg mri/parc2502dwi.nii.gz \ # parcellation extended & registered to dti_FA.nii.gz
--ctab colortable.txt \
--i $dtipath/$subj/dti_FA.nii.gz \
--excludeid 0 \
--sum ../FA/${subj}_fa.stats
cd ../
fi
done
but had so many zero values that I wanted to check first if I get values for all the parcels if I use the non-extended annot-file.
Thanks a lot for helping me with this problem! Cheers, Steph
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> Sent: Sunday, 9 December 2018 5:24 PM To: Freesurfer support list Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
Hi Steph
I think that mri_segstats would work, but I defer to Doug. The output
should be normal volume, viewable in freeview. I'm not sure why you would
want to do this with FA though. Maybe you could give us more details about
what you are trying to accomplish? Seems like you want to project the annot
into the volume, not the FA maps. Not sure if surf2vol takes annots, again
Doug would know
cheers.
Bruce
On Sun, 9 Dec
2018, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Dear Bruce,
Thanks for your quick and helpful reply!
Using the surface lh.white has worked perfectly.
Do I understand correctly that the output file is the FA volume conform
with the lh.white surface? Therefore, if I wanted to extract the mean FA
for each parcel I would use this newly created volume and the annotation
file? I had previously used mri_segstats, but that wouldn't work here. Is
that right?
Cheers,
Steph
-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Sunday, December 09, 2018 4:48 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [EXTERNAL] Re: [Freesurfer] mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
Hi Stephanie
the -so switch requirees a surface and an overlay. What you have given it is an annotation (NOT a surface) and an overlay. Use one of the surfaces instead (e.g. lh.white)
cheers
Bruce
On Sun, 9 Dec 2018,
Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Hi Freesurfers,
I’m trying to project the surface, a fine-grained parcellation
(?h.250.aparc.annot), into volume space (dti_FA) with
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
mri_surf2vol \
--o FA/annot2FA.nii.gz \
--subject $subj \
--so $SUBJECTS_DIR/$subj/label/lh.250.aparc.annot
$dtipath/$subj/dti_FA.nii.gz
cd ../
fi
done
However, I get ERROR: MRISread: file
‘$SUBJECTS_DIR/$subj/label/lh.250.aparc.annot’ has more faces than vertices!
How can I solve this?
Thanks,
Stephanie
Stephanie Winkelbeiner, MSc
Research Coordinator
Psychiatry Research
Zucker Hillside Hospital
75-59 263 Street
Glen Oaks, NY 11004
Tel: (718) 470-4588
Email: swinkelbei@northwell.edumailto:swinkelbei@northwell.edu
Northwell Health
Visit us at Northwell.edu
The information contained in this electronic e-mail transmission and
any attachments are intended only for the use of the individual or
entity to whom or to which it is addressed, and may contain
information that is privileged, confidential and exempt from
disclosure under applicable law. If the reader of this communication
is not the intended recipient, or the employee or agent responsible
for delivering this communication to the intended recipient, you are
hereby notified that any dissemination, distribution, copying or
disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium.
Receipt by anyone other than the intended recipient is not a waiver of
any attorney-client, physician-patient or other privilege.
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
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The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
_______________________________________________
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The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
It might be that the mri_aparc2aseg route requires two transformations (one to 1mm, then one to your DTI).
On 12/11/18 11:09 AM, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution Hi Doug,
Thanks a lot for getting back to me and your helpful comments! Good that you mention the mri_aparc2aseg option. I had tried that and registered the resulting volume aparc.250+2mm.nii.gz to DTI space (bbregister and mri_vol2vol). Yet, extracting the FA values (mri_segstats) resulted in >70% of parcels having zero values (with the label2vol approach I get values in almost all parcels). I checked, aparc.250+2mm.nii.gz and dti_FA.nii.gz seem to be perfectly coregistered. Could you think of any reason why that is?
Thanks, Steph
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, December 11, 2018 10:49 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
External Email. Use Caution. That all looks like it would work to me. Another thing you can try is the way we create the wmparc.mgz using mri_aparc2aseg. You can find the commandline in the recon-all.log file (make sure to set the output name so that you don't overwrite wmparc.mgz). You can specify the max distance away from cortex that the label can grow. On 12/10/18 5:06 PM, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution Hi Douglas,
I was wondering if I can use an annot file in surf2vol to project those parcels into the FA image space? Or would label2vol be more appropriate? Bruce was so kind to give me his advice already and we discussed my challenges a bit (see below).
Besides surf2vol with lh.white, I tried the following:
for subj in SPN01*; do if [ -d "${subj}" ]; then cd $subj/ mri_label2vol \ --annot label/lh.250.aparc.annot \ --temp $dtipath/$subj/dti_FA.nii.gz \ --reg mri/register.dat \ --proj abs -3 -2 .1 \ --subject $subj --hemi lh \ --o mri/vol250-lh.nii.gz cd ../ fi done
Then, I used the vol250-lh image with mri_segstats to get the FA values (see below). This gives reasonable FA values.
Would you consider this a valid approach?
I’d greatly appreciate your input. Cheers, Steph
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Winkelbeiner, Stephanie A Sent: Sunday, December 09, 2018 8:58 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
External Email - Use Caution
Hi Bruce,
you are exactly right. We are interested in projecting the parcellations into the WM to extract the corresponding FA values.
I had tried
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
# extract FA
mri_segstats \
--seg mri/parc2502dwi.nii.gz \ # parcellation extended & registered to dti_FA.nii.gz
--ctab colortable.txt \
--i $dtipath/$subj/dti_FA.nii.gz \
--excludeid 0 \
--sum ../FA/${subj}_fa.stats
cd ../
fi
done
but had so many zero values that I wanted to check first if I get values for all the parcels if I use the non-extended annot-file.
Thanks a lot for helping me with this problem! Cheers, Steph
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> Sent: Sunday, 9 December 2018 5:24 PM To: Freesurfer support list Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
Hi Steph
I think that mri_segstats would work, but I defer to Doug. The output
should be normal volume, viewable in freeview. I'm not sure why you would
want to do this with FA though. Maybe you could give us more details about
what you are trying to accomplish? Seems like you want to project the annot
into the volume, not the FA maps. Not sure if surf2vol takes annots, again
Doug would know
cheers.
Bruce
On Sun, 9 Dec
2018, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Dear Bruce,
Thanks for your quick and helpful reply!
Using the surface lh.white has worked perfectly.
Do I understand correctly that the output file is the FA volume conform
with the lh.white surface? Therefore, if I wanted to extract the mean FA
for each parcel I would use this newly created volume and the annotation
file? I had previously used mri_segstats, but that wouldn't work here. Is
that right?
Cheers,
Steph
-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Sunday, December 09, 2018 4:48 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [EXTERNAL] Re: [Freesurfer] mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
Hi Stephanie
the -so switch requirees a surface and an overlay. What you have given it is an annotation (NOT a surface) and an overlay. Use one of the surfaces instead (e.g. lh.white)
cheers
Bruce
On Sun, 9 Dec 2018,
Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Hi Freesurfers,
I’m trying to project the surface, a fine-grained parcellation
(?h.250.aparc.annot), into volume space (dti_FA) with
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
mri_surf2vol \
--o FA/annot2FA.nii.gz \
--subject $subj \
--so $SUBJECTS_DIR/$subj/label/lh.250.aparc.annot
$dtipath/$subj/dti_FA.nii.gz
cd ../
fi
done
However, I get ERROR: MRISread: file
‘$SUBJECTS_DIR/$subj/label/lh.250.aparc.annot’ has more faces than vertices!
How can I solve this?
Thanks,
Stephanie
Stephanie Winkelbeiner, MSc
Research Coordinator
Psychiatry Research
Zucker Hillside Hospital
75-59 263 Street
Glen Oaks, NY 11004
Tel: (718) 470-4588
Email: swinkelbei@northwell.edumailto:swinkelbei@northwell.edu
Northwell Health
Visit us at Northwell.edu
The information contained in this electronic e-mail transmission and
any attachments are intended only for the use of the individual or
entity to whom or to which it is addressed, and may contain
information that is privileged, confidential and exempt from
disclosure under applicable law. If the reader of this communication
is not the intended recipient, or the employee or agent responsible
for delivering this communication to the intended recipient, you are
hereby notified that any dissemination, distribution, copying or
disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium.
Receipt by anyone other than the intended recipient is not a waiver of
any attorney-client, physician-patient or other privilege.
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
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External Email - Use Caution
Great - I gonna try that straight away! Thanks a lot!
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, December 11, 2018 11:16 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices {Disarmed}
External Email. Use Caution. It might be that the mri_aparc2aseg route requires two transformations (one to 1mm, then one to your DTI). On 12/11/18 11:09 AM, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution Hi Doug,
Thanks a lot for getting back to me and your helpful comments! Good that you mention the mri_aparc2aseg option. I had tried that and registered the resulting volume aparc.250+2mm.nii.gz to DTI space (bbregister and mri_vol2vol). Yet, extracting the FA values (mri_segstats) resulted in >70% of parcels having zero values (with the label2vol approach I get values in almost all parcels). I checked, aparc.250+2mm.nii.gz and dti_FA.nii.gz seem to be perfectly coregistered. Could you think of any reason why that is?
Thanks, Steph
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, December 11, 2018 10:49 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
External Email. Use Caution. That all looks like it would work to me. Another thing you can try is the way we create the wmparc.mgz using mri_aparc2aseg. You can find the commandline in the recon-all.log file (make sure to set the output name so that you don't overwrite wmparc.mgz). You can specify the max distance away from cortex that the label can grow. On 12/10/18 5:06 PM, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution Hi Douglas,
I was wondering if I can use an annot file in surf2vol to project those parcels into the FA image space? Or would label2vol be more appropriate? Bruce was so kind to give me his advice already and we discussed my challenges a bit (see below).
Besides surf2vol with lh.white, I tried the following:
for subj in SPN01*; do if [ -d "${subj}" ]; then cd $subj/ mri_label2vol \ --annot label/lh.250.aparc.annot \ --temp $dtipath/$subj/dti_FA.nii.gz \ --reg mri/register.dat \ --proj abs -3 -2 .1 \ --subject $subj --hemi lh \ --o mri/vol250-lh.nii.gz cd ../ fi done
Then, I used the vol250-lh image with mri_segstats to get the FA values (see below). This gives reasonable FA values.
Would you consider this a valid approach?
I’d greatly appreciate your input. Cheers, Steph
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Winkelbeiner, Stephanie A Sent: Sunday, December 09, 2018 8:58 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
External Email - Use Caution
Hi Bruce,
you are exactly right. We are interested in projecting the parcellations into the WM to extract the corresponding FA values.
I had tried
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
# extract FA
mri_segstats \
--seg mri/parc2502dwi.nii.gz \ # parcellation extended & registered to dti_FA.nii.gz
--ctab colortable.txt \
--i $dtipath/$subj/dti_FA.nii.gz \
--excludeid 0 \
--sum ../FA/${subj}_fa.stats
cd ../
fi
done
but had so many zero values that I wanted to check first if I get values for all the parcels if I use the non-extended annot-file.
Thanks a lot for helping me with this problem! Cheers, Steph
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> Sent: Sunday, 9 December 2018 5:24 PM To: Freesurfer support list Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
Hi Steph
I think that mri_segstats would work, but I defer to Doug. The output
should be normal volume, viewable in freeview. I'm not sure why you would
want to do this with FA though. Maybe you could give us more details about
what you are trying to accomplish? Seems like you want to project the annot
into the volume, not the FA maps. Not sure if surf2vol takes annots, again
Doug would know
cheers.
Bruce
On Sun, 9 Dec
2018, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Dear Bruce,
Thanks for your quick and helpful reply!
Using the surface lh.white has worked perfectly.
Do I understand correctly that the output file is the FA volume conform
with the lh.white surface? Therefore, if I wanted to extract the mean FA
for each parcel I would use this newly created volume and the annotation
file? I had previously used mri_segstats, but that wouldn't work here. Is
that right?
Cheers,
Steph
-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Sunday, December 09, 2018 4:48 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [EXTERNAL] Re: [Freesurfer] mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
Hi Stephanie
the -so switch requirees a surface and an overlay. What you have given it is an annotation (NOT a surface) and an overlay. Use one of the surfaces instead (e.g. lh.white)
cheers
Bruce
On Sun, 9 Dec 2018,
Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Hi Freesurfers,
I’m trying to project the surface, a fine-grained parcellation
(?h.250.aparc.annot), into volume space (dti_FA) with
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
mri_surf2vol \
--o FA/annot2FA.nii.gz \
--subject $subj \
--so $SUBJECTS_DIR/$subj/label/lh.250.aparc.annot
$dtipath/$subj/dti_FA.nii.gz
cd ../
fi
done
However, I get ERROR: MRISread: file
‘$SUBJECTS_DIR/$subj/label/lh.250.aparc.annot’ has more faces than vertices!
How can I solve this?
Thanks,
Stephanie
Stephanie Winkelbeiner, MSc
Research Coordinator
Psychiatry Research
Zucker Hillside Hospital
75-59 263 Street
Glen Oaks, NY 11004
Tel: (718) 470-4588
Email: swinkelbei@northwell.edumailto:swinkelbei@northwell.edu
Northwell Health
Visit us at Northwell.edu
The information contained in this electronic e-mail transmission and
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information that is privileged, confidential and exempt from
disclosure under applicable law. If the reader of this communication
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External Email - Use Caution
Hi Doug & Bruce,
Thanks again to both of your for your help!
I ended up using label2vol to extend the parcels into the wm and register them to DTI space. Using mri_segstats with an FA_skeletonised mask and the dti_FA.nii.gz image, I get reasonable WM values. However, for some of the subjects I get more 0 values in the left than the right hemisphere.
I would have expected to get values for all the parcels or at least zero values consistently for some parcels as I registered all parcels to the individual subjects dti_FA.nii.gz image.
Am I missing something?
Thanks, Steph
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, December 11, 2018 11:16 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices {Disarmed}
External Email. Use Caution. It might be that the mri_aparc2aseg route requires two transformations (one to 1mm, then one to your DTI). On 12/11/18 11:09 AM, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution Hi Doug,
Thanks a lot for getting back to me and your helpful comments! Good that you mention the mri_aparc2aseg option. I had tried that and registered the resulting volume aparc.250+2mm.nii.gz to DTI space (bbregister and mri_vol2vol). Yet, extracting the FA values (mri_segstats) resulted in >70% of parcels having zero values (with the label2vol approach I get values in almost all parcels). I checked, aparc.250+2mm.nii.gz and dti_FA.nii.gz seem to be perfectly coregistered. Could you think of any reason why that is?
Thanks, Steph
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, December 11, 2018 10:49 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
External Email. Use Caution. That all looks like it would work to me. Another thing you can try is the way we create the wmparc.mgz using mri_aparc2aseg. You can find the commandline in the recon-all.log file (make sure to set the output name so that you don't overwrite wmparc.mgz). You can specify the max distance away from cortex that the label can grow. On 12/10/18 5:06 PM, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution Hi Douglas,
I was wondering if I can use an annot file in surf2vol to project those parcels into the FA image space? Or would label2vol be more appropriate? Bruce was so kind to give me his advice already and we discussed my challenges a bit (see below).
Besides surf2vol with lh.white, I tried the following:
for subj in SPN01*; do if [ -d "${subj}" ]; then cd $subj/ mri_label2vol \ --annot label/lh.250.aparc.annot \ --temp $dtipath/$subj/dti_FA.nii.gz \ --reg mri/register.dat \ --proj abs -3 -2 .1 \ --subject $subj --hemi lh \ --o mri/vol250-lh.nii.gz cd ../ fi done
Then, I used the vol250-lh image with mri_segstats to get the FA values (see below). This gives reasonable FA values.
Would you consider this a valid approach?
I’d greatly appreciate your input. Cheers, Steph
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Winkelbeiner, Stephanie A Sent: Sunday, December 09, 2018 8:58 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
External Email - Use Caution
Hi Bruce,
you are exactly right. We are interested in projecting the parcellations into the WM to extract the corresponding FA values.
I had tried
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
# extract FA
mri_segstats \
--seg mri/parc2502dwi.nii.gz \ # parcellation extended & registered to dti_FA.nii.gz
--ctab colortable.txt \
--i $dtipath/$subj/dti_FA.nii.gz \
--excludeid 0 \
--sum ../FA/${subj}_fa.stats
cd ../
fi
done
but had so many zero values that I wanted to check first if I get values for all the parcels if I use the non-extended annot-file.
Thanks a lot for helping me with this problem! Cheers, Steph
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> Sent: Sunday, 9 December 2018 5:24 PM To: Freesurfer support list Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
Hi Steph
I think that mri_segstats would work, but I defer to Doug. The output
should be normal volume, viewable in freeview. I'm not sure why you would
want to do this with FA though. Maybe you could give us more details about
what you are trying to accomplish? Seems like you want to project the annot
into the volume, not the FA maps. Not sure if surf2vol takes annots, again
Doug would know
cheers.
Bruce
On Sun, 9 Dec
2018, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Dear Bruce,
Thanks for your quick and helpful reply!
Using the surface lh.white has worked perfectly.
Do I understand correctly that the output file is the FA volume conform
with the lh.white surface? Therefore, if I wanted to extract the mean FA
for each parcel I would use this newly created volume and the annotation
file? I had previously used mri_segstats, but that wouldn't work here. Is
that right?
Cheers,
Steph
-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Sunday, December 09, 2018 4:48 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [EXTERNAL] Re: [Freesurfer] mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
Hi Stephanie
the -so switch requirees a surface and an overlay. What you have given it is an annotation (NOT a surface) and an overlay. Use one of the surfaces instead (e.g. lh.white)
cheers
Bruce
On Sun, 9 Dec 2018,
Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Hi Freesurfers,
I’m trying to project the surface, a fine-grained parcellation
(?h.250.aparc.annot), into volume space (dti_FA) with
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
mri_surf2vol \
--o FA/annot2FA.nii.gz \
--subject $subj \
--so $SUBJECTS_DIR/$subj/label/lh.250.aparc.annot
$dtipath/$subj/dti_FA.nii.gz
cd ../
fi
done
However, I get ERROR: MRISread: file
‘$SUBJECTS_DIR/$subj/label/lh.250.aparc.annot’ has more faces than vertices!
How can I solve this?
Thanks,
Stephanie
Stephanie Winkelbeiner, MSc
Research Coordinator
Psychiatry Research
Zucker Hillside Hospital
75-59 263 Street
Glen Oaks, NY 11004
Tel: (718) 470-4588
Email: swinkelbei@northwell.edumailto:swinkelbei@northwell.edu
Northwell Health
Visit us at Northwell.edu
The information contained in this electronic e-mail transmission and
any attachments are intended only for the use of the individual or
entity to whom or to which it is addressed, and may contain
information that is privileged, confidential and exempt from
disclosure under applicable law. If the reader of this communication
is not the intended recipient, or the employee or agent responsible
for delivering this communication to the intended recipient, you are
hereby notified that any dissemination, distribution, copying or
disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium.
Receipt by anyone other than the intended recipient is not a waiver of
any attorney-client, physician-patient or other privilege.
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
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My bad, I found that the output file from label2vol, vol250-?h.nii.gz, is not oriented correctly when I view it in fsleyes... Trying fslorient2std left vol250-?h.nii.gz totally un-impressed with the same orientation as before. Fslswapdim also doesn't seem to do the trick.
Would it make more sense to reorient the DTI images to freesurfer space since I'm using a freesurfer command to extract values anyway?
Or which command would be appropriate to get vol250-?h.nii.gz into fsl space? This I should probably ask in the fsl mailing list, I guess.
Would you have some advice nonetheless?
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Winkelbeiner, Stephanie A Sent: Friday, December 14, 2018 4:46 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices {Disarmed} {Disarmed}
External Email. Use Caution.
External Email - Use Caution Hi Doug & Bruce,
Thanks again to both of your for your help!
I ended up using label2vol to extend the parcels into the wm and register them to DTI space. Using mri_segstats with an FA_skeletonised mask and the dti_FA.nii.gz image, I get reasonable WM values. However, for some of the subjects I get more 0 values in the left than the right hemisphere.
I would have expected to get values for all the parcels or at least zero values consistently for some parcels as I registered all parcels to the individual subjects dti_FA.nii.gz image.
Am I missing something?
Thanks, Steph
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, December 11, 2018 11:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices {Disarmed}
External Email. Use Caution. It might be that the mri_aparc2aseg route requires two transformations (one to 1mm, then one to your DTI). On 12/11/18 11:09 AM, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution Hi Doug,
Thanks a lot for getting back to me and your helpful comments! Good that you mention the mri_aparc2aseg option. I had tried that and registered the resulting volume aparc.250+2mm.nii.gz to DTI space (bbregister and mri_vol2vol). Yet, extracting the FA values (mri_segstats) resulted in >70% of parcels having zero values (with the label2vol approach I get values in almost all parcels). I checked, aparc.250+2mm.nii.gz and dti_FA.nii.gz seem to be perfectly coregistered. Could you think of any reason why that is?
Thanks, Steph
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, December 11, 2018 10:49 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
External Email. Use Caution. That all looks like it would work to me. Another thing you can try is the way we create the wmparc.mgz using mri_aparc2aseg. You can find the commandline in the recon-all.log file (make sure to set the output name so that you don't overwrite wmparc.mgz). You can specify the max distance away from cortex that the label can grow. On 12/10/18 5:06 PM, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution Hi Douglas,
I was wondering if I can use an annot file in surf2vol to project those parcels into the FA image space? Or would label2vol be more appropriate? Bruce was so kind to give me his advice already and we discussed my challenges a bit (see below).
Besides surf2vol with lh.white, I tried the following:
for subj in SPN01*; do if [ -d "${subj}" ]; then cd $subj/ mri_label2vol \ --annot label/lh.250.aparc.annot \ --temp $dtipath/$subj/dti_FA.nii.gz \ --reg mri/register.dat \ --proj abs -3 -2 .1 \ --subject $subj --hemi lh \ --o mri/vol250-lh.nii.gz cd ../ fi done
Then, I used the vol250-lh image with mri_segstats to get the FA values (see below). This gives reasonable FA values.
Would you consider this a valid approach?
I’d greatly appreciate your input. Cheers, Steph
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Winkelbeiner, Stephanie A Sent: Sunday, December 09, 2018 8:58 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
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Hi Bruce,
you are exactly right. We are interested in projecting the parcellations into the WM to extract the corresponding FA values.
I had tried
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
# extract FA
mri_segstats \
--seg mri/parc2502dwi.nii.gz \ # parcellation extended & registered to dti_FA.nii.gz
--ctab colortable.txt \
--i $dtipath/$subj/dti_FA.nii.gz \
--excludeid 0 \
--sum ../FA/${subj}_fa.stats
cd ../
fi
done
but had so many zero values that I wanted to check first if I get values for all the parcels if I use the non-extended annot-file.
Thanks a lot for helping me with this problem! Cheers, Steph
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> Sent: Sunday, 9 December 2018 5:24 PM To: Freesurfer support list Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
Hi Steph
I think that mri_segstats would work, but I defer to Doug. The output
should be normal volume, viewable in freeview. I'm not sure why you would
want to do this with FA though. Maybe you could give us more details about
what you are trying to accomplish? Seems like you want to project the annot
into the volume, not the FA maps. Not sure if surf2vol takes annots, again
Doug would know
cheers.
Bruce
On Sun, 9 Dec
2018, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Dear Bruce,
Thanks for your quick and helpful reply!
Using the surface lh.white has worked perfectly.
Do I understand correctly that the output file is the FA volume conform
with the lh.white surface? Therefore, if I wanted to extract the mean FA
for each parcel I would use this newly created volume and the annotation
file? I had previously used mri_segstats, but that wouldn't work here. Is
that right?
Cheers,
Steph
-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Sunday, December 09, 2018 4:48 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [EXTERNAL] Re: [Freesurfer] mri_surf2vol: has many more faces than vertices
External Email. Use Caution.
Hi Stephanie
the -so switch requirees a surface and an overlay. What you have given it is an annotation (NOT a surface) and an overlay. Use one of the surfaces instead (e.g. lh.white)
cheers
Bruce
On Sun, 9 Dec 2018,
Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Hi Freesurfers,
I’m trying to project the surface, a fine-grained parcellation
(?h.250.aparc.annot), into volume space (dti_FA) with
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
mri_surf2vol \
--o FA/annot2FA.nii.gz \
--subject $subj \
--so $SUBJECTS_DIR/$subj/label/lh.250.aparc.annot
$dtipath/$subj/dti_FA.nii.gz
cd ../
fi
done
However, I get ERROR: MRISread: file
‘$SUBJECTS_DIR/$subj/label/lh.250.aparc.annot’ has more faces than vertices!
How can I solve this?
Thanks,
Stephanie
Stephanie Winkelbeiner, MSc
Research Coordinator
Psychiatry Research
Zucker Hillside Hospital
75-59 263 Street
Glen Oaks, NY 11004
Tel: (718) 470-4588
Email: swinkelbei@northwell.edumailto:swinkelbei@northwell.edu
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-
Bruce Fischl -
Greve, Douglas N.,Ph.D. -
Winkelbeiner, Stephanie A