Re: [Freesurfer] Are two T1 scans helpful for better recon-all?
Hi Hai, I agree with Bruce. In a recent paper (http://www.ncbi.nlm.nih.gov/pubmed/23668971), for a variety of 3T vendor and coil configurations, we confirmed previous findings that averaging two within-session uncorrupted MPRAGE scans did not significantly improve across session reproducibility. In you case just choose the best one of the two. Is it worth acquiring two MPRAGES then? Tricky. Maybe you can go for only a single acquistion if your MR operator is experienced to distinguish what level of artifact will be unacceptable for the target analysis and deserves a repeated acquisition in case of unacceptable quality. Otherwise, one may fix two acquisitions in the protocol and use the best of them. Nevertheless, the operators should always be paying attention to the data quality during the acquisition to decide if some type of intervention can help. cheers, jorge On 06/01/2014 21:38, Bruce Fischl wrote: Hi Hai it really depends on your coil and field strength, and whether either is motion-corrupted. For 3T 32 channel data our somewhat ad hoc opinion is that one is better than two (due to blurring induced by interpolation), but it's really a case-by-case decision. sorry that there isn't an easier answer Bruce On Mon, 6 Jan 2014, Hai Pan wrote: Hello, FreeSurfer experts, We made two T1 scans for each subject at each session, will they be helpful for better recon-all results? Shall I average them and process the averaged T1 image? Let me know please. Thank you, Hai ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jorge Jovicich, Ph.D. MR Lab Coordinator Center for Mind Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovic...@unitn.it http://www.cimec.unitn.it/ http://polorovereto.unitn.it/~jovicich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Question about 7T MRI Datasets with isotropic voxels of 0, 7 mm
Hi, we are currently using Freesurfer for a complete segmentation of 7T MRI Datasets with isotropic voxels of 0,7 mm. Now the question has come up whether Freesurfer calculates with this original submilimeter resolution or if it internally reslices our data (e.g. to 1mm), which could result in a loss of quality. If so, is it possible to change Freesurfers settings to obtain optimal results from the segmentation? Any help would be greatly appreciated, best regards, Valentin Frank ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
Hi Muhammad have you looked at the help? It's pretty extensive. If you have trouble post again and Doug should be able to guide you cheers Bruce On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote: Thank you Bruce, Please guide me how can I use mri_surf2vol command on lh/rh.thickness files to get the output as lh/rh.ribbon.nii for AFNI SUMA. Thank you Best Regards, Muhammad Naveed Iqbal Qureshi From: freesurfer-requ...@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 119, Issue 6 To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 6 Jan 2014 10:51:33 -0500 Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than Re: Contents of Freesurfer digest... Today's Topics: 1. erroneuos segmentation labeling of skull outside of brain (Yuliya Yoncheva) 2. Re: erroneuos segmentation labeling of skull outside of brain (Bruce Fischl) 3. Re: Motion correction for SPACE FLAIR (Bruce Fischl) 4. Re: erroneuos segmentation labeling of skull outside of brain (Yuliya Yoncheva) 5. Re: erroneuos segmentation labeling of skull outside of brain (Bruce Fischl) 6. Re: recon-all exited w/errors (Bruce Fischl) 7. ROI masks created in FreeSurfer used in FSL?? (Frank Hsieh) 8. converting .thickness files of T1 MRI from FreeSurfer into AFNI (Muhammad Naveed Iqbal Qureshi) 9. brain orientation in qdec (L. Schweren) 10. Re: converting .thickness files of T1 MRI from FreeSurfer into AFNI (Bruce Fischl) 11. recon-all error (Emad Ahmadi) 12. Fwd: Anatomical segmentation - question (Rotem Saar) -- Message: 1 Date: Sun, 5 Jan 2014 15:14:39 -0500 From: Yuliya Yoncheva yuliya.yonch...@gmail.com Subject: [Freesurfer] erroneuos segmentation labeling of skull outside of brain To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jy...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Dear FreeSurfer community, I am visually inspecting the quality of my recon -all output for a large dataset and have a rookie question. In some instances, when skull stripping ended up leaving some of the skull, these voxels are associated with a sgmtn label (cerebral cortex). In other instances, although there are a small number of skull voxels that were not removed automatically, these voxels do not have an associated sgmnt label available in TkMedit Tools. Is it the case that only the voxels for which there is a segmentation label are actually added to the total grey volume estimate? Thus, voxels, which have not been automatically labelled would not impact volume computations? Thank you kindly for your help. -- next part -- An HTML attachment was scrubbed... URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140105/3 92deba7/attachment-0001.html -- next part -- A non-text attachment was scrubbed... Name: ExCerCor.png Type: image/png Size: 81100 bytes Desc: not available Url :http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140105/3 92deba7/attachment-0001.png -- Message: 2 Date: Sun, 5 Jan 2014 15:40:24 -0500 (EST) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull outside of brain To: Yuliya Yoncheva yuliya.yonch...@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.03.1401051539450.16...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=iso-8859-1 Hi Yuliya they are included if they are inside of the ?h.pial surface. We don't use the cortex aseg label as it is in general less accurate than the surfaces. cheers Bruce On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: Dear FreeSurfer community, I am visually inspecting the quality of my recon -all output for a large dataset and have a rookie question. In some instances, when skull stripping ended up leaving some of the skull, these voxels are associated with a sgmtn label (cerebral cortex). In other instances, although there are a small number of skull voxels that were not removed automatically, these voxels do not have an associated sgmnt label available in TkMedit Tools. Is it the case that only the voxels for which there is a segmentation label are actually added to the total grey volume estimate?? Thus, voxels, which have not been automatically labelled would not impact volume computations? Thank you kindly for your help. -- Message: 3
Re: [Freesurfer] Are two T1 scans helpful for better recon-all?
thanks Jorge, nice to see that someone quantified this :) Bruce On Tue, 7 Jan 2014, Jorge Jovicich wrote: Hi Hai, I agree with Bruce. In a recent paper (http://www.ncbi.nlm.nih.gov/pubmed/23668971), for a variety of 3T vendor and coil configurations, we confirmed previous findings that averaging two within-session uncorrupted MPRAGE scans did not significantly improve across session reproducibility. In you case just choose the best one of the two. Is it worth acquiring two MPRAGES then? Tricky. Maybe you can go for only a single acquistion if your MR operator is experienced to distinguish what level of artifact will be unacceptable for the target analysis and deserves a repeated acquisition in case of unacceptable quality. Otherwise, one may fix two acquisitions in the protocol and use the best of them. Nevertheless, the operators should always be paying attention to the data quality during the acquisition to decide if some type of intervention can help. cheers, jorge On 06/01/2014 21:38, Bruce Fischl wrote: Hi Hai it really depends on your coil and field strength, and whether either is motion-corrupted. For 3T 32 channel data our somewhat ad hoc opinion is that one is better than two (due to blurring induced by interpolation), but it's really a case-by-case decision. sorry that there isn't an easier answer Bruce On Mon, 6 Jan 2014, Hai Pan wrote: Hello, FreeSurfer experts, We made two T1 scans for each subject at each session, will they be helpful for better recon-all results? Shall I average them and process the averaged T1 image? Let me know please. Thank you, Hai ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Question about 7T MRI Datasets with isotropic voxels of 0, 7 mm
Hi Valentin we do reslice it for the basic processing, but you can do post-hoc surface deformation and things like hippocampal subfield segmentation at the native resolution. Or you can use the -cm switch to prevent the reslicing, but it is something we don't have a ton of experience with. cheers Bruce On Tue, 7 Jan 2014, Valentin Frank wrote: Hi, we are currently using Freesurfer for a complete segmentation of 7T MRI Datasets with isotropic voxels of 0,7 mm. Now the question has come up whether Freesurfer calculates with this original submilimeter resolution or if it internally reslices our data (e.g. to 1mm), which could result in a loss of quality. If so, is it possible to change Freesurfers settings to obtain optimal results from the segmentation? Any help would be greatly appreciated, best regards, Valentin Frank ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
try adding paint after surf/rh.thickness. The -surfval switch takes an
optional format parameter after the file name I think
cheers
Bruce
On Tue, 7 Jan 2014, Muhammad
Naveed Iqbal Qureshi wrote:
Hi Bruce,
I have tried to convert by using the following commands but still some error
occur.
UN:~ set subj=/home/naveed/freesurfer/subjects/CHR01/
UN:~ mri_surf2vol --surfval surf/rh.thickness --hemi rh --fillribbon
--template mri/orig.mgz --volregidentity {$subj} --outvol
{$subj}_rh.ribbon.nii
gdiagno = -1
ERROR: cannot recognize the type of surf/rh.thickness
Can you help me.
Thank you.
Best Regards,
Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:13:45 -0500
From: fis...@nmr.mgh.harvard.edu
To: mniqure...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
Hi Muhammad
have you looked at the help? It's pretty extensive. If you have trouble
post again and Doug should be able to guide you
cheers
Bruce
On Tue, 7 Jan 2014, Muhammad
Naveed Iqbal Qureshi wrote:
Thank you Bruce,
Please guide me how can I use mri_surf2vol command on lh/rh.thickness
files
to get the output as lh/rh.ribbon.nii for AFNI SUMA.
Thank you
Best Regards,
Muhammad Naveed Iqbal Qureshi
From: freesurfer-requ...@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 119, Issue 6
To: freesurfer@nmr.mgh.harvard.edu
Date: Mon, 6 Jan 2014 10:51:33 -0500
Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu
You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific
than Re: Contents of Freesurfer digest...
Today's Topics:
1. erroneuos segmentation labeling of skull outside of brain
(Yuliya Yoncheva)
2. Re: erroneuos segmentation labeling of skull outside of brain
(Bruce Fischl)
3. Re: Motion correction for SPACE FLAIR (Bruce Fischl)
4. Re: erroneuos segmentation labeling of skull outside of brain
(Yuliya Yoncheva)
5. Re: erroneuos segmentation labeling of skull outside of brain
(Bruce Fischl)
6. Re: recon-all exited w/errors (Bruce Fischl)
7. ROI masks created in FreeSurfer used in FSL?? (Frank Hsieh)
8. converting .thickness files of T1 MRI from FreeSurfer into
AFNI (Muhammad Naveed Iqbal Qureshi)
9. brain orientation in qdec (L. Schweren)
10. Re: converting .thickness files of T1 MRI from FreeSurfer
into AFNI (Bruce Fischl)
11. recon-all error (Emad Ahmadi)
12. Fwd: Anatomical segmentation - question (Rotem Saar)
--
Message: 1
Date: Sun, 5 Jan 2014 15:14:39 -0500
From: Yuliya Yoncheva yuliya.yonch...@gmail.com
Subject: [Freesurfer] erroneuos segmentation labeling of skull outside
of brain
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jy...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1
Dear FreeSurfer community,
I am visually inspecting the quality of my recon -all output for a
large
dataset and have a rookie question.
In some instances, when skull stripping ended up leaving some of the
skull,
these voxels are associated with a sgmtn label (cerebral cortex). In
other instances, although there are a small number of skull voxels
that
were not removed automatically, these voxels do not have an associated
sgmnt label available in TkMedit Tools.
Is it the case that only the voxels for which there is a segmentation
label
are actually added to the total grey volume estimate?
Thus, voxels, which have not been automatically labelled would not
impact
volume computations?
Thank you kindly for your help.
-- next part --
An HTML attachment was scrubbed...
URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201401
05/3
92deba7/attachment-0001.html
-- next part --
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Name: ExCerCor.png
Type: image/png
Size: 81100 bytes
Desc: not available
Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20140105/
3
92deba7/attachment-0001.png
--
Message: 2
Date: Sun, 5 Jan 2014 15:40:24 -0500 (EST)
From: Bruce Fischl fis...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull
outside of brain
To: Yuliya Yoncheva yuliya.yonch...@gmail.com
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID: alpine.lrh.2.03.1401051539450.16...@nmr.mgh.harvard.edu
Content-Type:
Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
does mri/orig.mgz exist?
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi
wrote:
Now another error
UN:~ mri_surf2vol --surfval surf/rh.thickness paint --hemi rh --fillribbon
--template mri/orig.mgz --volregidentity {$subj} --outvol
{$subj}_rh.ribbon.nii
gdiagno = -1
Using identity matrix for registration
mghRead(mri/orig.mgz, -1): could not open file
mri_surf2vol ERROR: reading mri/orig.mgz header
Best Regards,
Muhammad Naveed Iqbal Qureshi
Ph.D. Candidate
Bio-Medical Signal System Analysis Laboratory
Department of Medical System Engineering
Gwangju Institute of Sciences and Technology
123, Cheomdangwagi-ro, Buk-gu, Gwangju, 500-712, Republic of Korea
Tel : +82-62-715-3266
Email : mniqure...@gist.ac.kr
URL : http://bmssa.gist.ac.kr
P please don't print this e-mail unless you really need to
Date: Tue, 7 Jan 2014 08:26:56 -0500
From: fis...@nmr.mgh.harvard.edu
To: mniqure...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
sorry, I wasn't clear. Try:
mri_surf2vol --surfval surf/rh.thickness paint --hemi rh --fillribbon \
--template mri/orig.mgz --volregidentity {$subj} --outvol
{$subj}_rh.ribbon.nii
On
Tue, 7 Jan 2014, Muhammad Naveed Iqbal
Qureshi wrote:
Still the same error
UN:~ mri_surf2vol --surfval surf/rh.thickness.paint --hemi rh
--fillribbon
--template mri/orig.mgz --volregidentity {$subj} --outvol
{$subj}_rh.ribbon.nii
gdiagno = -1
ERROR: cannot recognize the type of surf/rh.thickness.paint
Best Regards,
Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:20:43 -0500
From: fis...@nmr.mgh.harvard.edu
To: mniqure...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
try adding paint after surf/rh.thickness. The -surfval switch
takes an
optional format parameter after the file name I think
cheers
Bruce
On Tue, 7 Jan 2014, Muhammad
Naveed Iqbal Qureshi wrote:
Hi Bruce,
I have tried to convert by using the following commands but still
some
error
occur.
UN:~ set subj=/home/naveed/freesurfer/subjects/CHR01/
UN:~ mri_surf2vol --surfval surf/rh.thickness --hemi rh
--fillribbon
--template mri/orig.mgz --volregidentity {$subj} --outvol
{$subj}_rh.ribbon.nii
gdiagno = -1
ERROR: cannot recognize the type of surf/rh.thickness
Can you help me.
Thank you.
Best Regards,
Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:13:45 -0500
From: fis...@nmr.mgh.harvard.edu
To: mniqure...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
Hi Muhammad
have you looked at the help? It's pretty extensive. If you have
trouble
post again and Doug should be able to guide you
cheers
Bruce
On Tue, 7 Jan 2014, Muhammad
Naveed Iqbal Qureshi wrote:
Thank you Bruce,
Please guide me how can I use mri_surf2vol command on
lh/rh.thickness
files
to get the output as lh/rh.ribbon.nii for AFNI SUMA.
Thank you
Best Regards,
Muhammad Naveed Iqbal Qureshi
From: freesurfer-requ...@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 119, Issue 6
To: freesurfer@nmr.mgh.harvard.edu
Date: Mon, 6 Jan 2014 10:51:33 -0500
Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu
You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more
specific
than Re: Contents of Freesurfer digest...
Today's Topics:
1. erroneuos segmentation labeling of skull outside of brain
(Yuliya Yoncheva)
2. Re: erroneuos segmentation labeling of skull outside of
brain
(Bruce Fischl)
3. Re: Motion correction for SPACE FLAIR (Bruce Fischl)
4. Re: erroneuos segmentation labeling of skull outside of
brain
(Yuliya Yoncheva)
5. Re: erroneuos segmentation labeling of skull outside of
brain
(Bruce Fischl)
6. Re: recon-all exited w/errors (Bruce Fischl)
7. ROI masks created in FreeSurfer used in FSL?? (Frank Hsieh)
8. converting .thickness files of T1 MRI from FreeSurfer into
AFNI (Muhammad Naveed Iqbal Qureshi)
9. brain orientation in qdec (L. Schweren)
10. Re: converting .thickness files of T1 MRI from FreeSurfer
into AFNI (Bruce Fischl)
11. recon-all error (Emad Ahmadi)
[Freesurfer] group analysis of functional data in custom volume space
Hi Freesurfer Experts, I would like to do a whole brain group analysis of functional data with mri_glmfit using a custom volume space instead of the MNI space Freesurfer provides. This is for primate data. I was wondering what the best way to do this would be. I have a T1 template in volume space to which I can align my functional data. I was thinking in getting registration files for the EPI to T1 alignment first, then to run mkanalysis-sess in native space per subject, the selxavg3-sess, then isxconcat-sess providing the registration files with the -reg flag, and then mri_glmfit. Does that make sense? Thank you very much, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Are two T1 scans helpful for better recon-all?
Hi Jorge, Thank you very much for your explanation. That's really helpful. Thank you, Hai On Tue, Jan 7, 2014 at 5:25 AM, Jorge Jovicich jorge.jovic...@unitn.itwrote: Hi Hai, I agree with Bruce. In a recent paper (http://www.ncbi.nlm.nih.gov/ pubmed/23668971), for a variety of 3T vendor and coil configurations, we confirmed previous findings that averaging two within-session uncorrupted MPRAGE scans did not significantly improve across session reproducibility. In you case just choose the best one of the two. Is it worth acquiring two MPRAGES then? Tricky. Maybe you can go for only a single acquistion if your MR operator is experienced to distinguish what level of artifact will be unacceptable for the target analysis and deserves a repeated acquisition in case of unacceptable quality. Otherwise, one may fix two acquisitions in the protocol and use the best of them. Nevertheless, the operators should always be paying attention to the data quality during the acquisition to decide if some type of intervention can help. cheers, jorge On 06/01/2014 21:38, Bruce Fischl wrote: Hi Hai it really depends on your coil and field strength, and whether either is motion-corrupted. For 3T 32 channel data our somewhat ad hoc opinion is that one is better than two (due to blurring induced by interpolation), but it's really a case-by-case decision. sorry that there isn't an easier answer Bruce On Mon, 6 Jan 2014, Hai Pan wrote: Hello, FreeSurfer experts, We made two T1 scans for each subject at each session, will they be helpful for better recon-all results? Shall I average them and process the averaged T1 image? Let me know please. Thank you, Hai ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jorge Jovicich, Ph.D. MR Lab Coordinator Center for Mind Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovic...@unitn.it http://www.cimec.unitn.it/ http://polorovereto.unitn.it/~jovicich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Transform sig.mgh file from fsaverage space into a subject's native space
Dear FS expert I tried to transform a sig.mgh file from fsaverage space into a subject's (called SCC1069) native space, but have some problems. I used: tkregister2 --mov fsaverage/mri/brain.mgz --targ SCC1069/mri/rawavg.mgz --regheader --reg register.dat mri_surf2surf --sval-xyz fsaverage/surf/pial --reg register.dat SCC1069/mri/rawavg.mgz --tval SCC1069/surf/pial.native --tval-xyz --hemi lh --s fsaverage If this is right, how can I proceed in order to transform the sig.cluster.mgh file produced by the MC simulations into the native space of subject SCC1069? Thanks in advance Regards Jürgen Hänggi Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] longitudinal hippocampal subfields analysis
Hi Salil, just run the hippo-subfields on the longitudinal results like this: recon-all -long tpNi templateid -hippo-subfields to generate the subfield data. I am not familiar with the kvlQuantify... script and think it works on all subjects in the Subjects dir. Not sure what the best way is to solve this as your subject dir contains also the cross and base results. Probably you can run the script and it will simply skip the cross and base directories (as no -hippo-subfields was run on them). Best, Martin On 01/05/2014 01:40 AM, Salil Soman wrote: Hi, I have been able to do the longitudinal processing steps for a number of subjects with 3 time points each, and then extract the generated statistics using aparcstats2table and asegstats2table. Is it possible to perform longitudinal analysis of the hippocampal subfields? If so, could someone point me to how to perform this analysis, as kvlQuantifyHippocampalSubfieldSegmentations.sh does not work on the output files I've generated. Thank you. Salil Soman, MD, MS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Problematic dilated ventricles
Hi Victor for each subject I think you want to run: set mdir=$SUBJECTS_DIR/$subject/mri mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \ -lta $mdir/transforms/cc_up.lta $subject cp aseg.auto.mgz aseg.mgz then run recon-all from normalization2 forward (check the recon-all -help for these steps) cheers Bruce On Tue, 7 Jan 2014, Victor Kovac wrote: Hi Bruce, I ran recon-all -autorecon2-cp -autorecon3 -s MPS1036-1 but, again, this did not affect the pial or wm surfaces. I have attached the recon-all.log in case that would be helpful in diagnosing the issue. Any advise would be greatly appreciated. Thanks! Victor On Thu, Jan 2, 2014 at 12:12 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Victor you can look in the recon-all -help and run the stages that are after mri_ca_label. Not sure why -make all didn't work, perhaps Zeke and/or Nick can comment? Bruce On Thu, 2 Jan 2014, Victor Kovac wrote: Dear Bruce, A few weeks ago you made code mods to mri_em_register and got recon-all to process a subject of mine, MPS1036-1. You sent me the new aseg.auto_noCCseg.mgz and told me to run recon-all -make all -s MPS1036-1. I did this but I get the message make: Nothing to be done for 'all' and when I visualize the segmentation with tkmedit, there appears to be no change to the pial or wm surfaces. Could you please advise? Thank you. Victor On Mon, Dec 9, 2013 at 2:11 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: if you rename aseg.auto_noCCseg.new.mgz to be aseg.auto_noCCseg.mgz then run: recon-all -make all -s MPS1036-1 you should be all set Bruce On Mon, 9 Dec 2013, Victor Kovac wrote: I was hoping to MPS1036-1. I only got aseg.auto_noCCseg.new.mgz. Thank you for looking into MPS2002-3 -- it is quite the brain. And somehow, with all those morphological abnormalities, this subject has an IQ of 130. Very strange. Thanks, Victor On Mon, Dec 9, 2013 at 2:03 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: which one? I'm still messing with MPS2002-3 in my spare time On Mon, 9 Dec 2013, Victor Kovac wrote: Hi Bruce, Is there a way for you to send the subject(s) you analyzed to me? I know it's too big for email, but could you possibly upload it to GoogleDrive? Thanks! Victor On Wed, Dec 4, 2013 at 3:40 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: p.s. the other thing I did was run the graph cut skull stripping, which removed a bunch of extraneous stuff On Wed, 4 Dec 2013, kovac...@umn.edu wrote: Hey! Victor Kovac (kovac...@umn.edu) has uploaded some files for you at the Martinos Center FileDrop: - MPS2002-3.zip (292.12 MiB) http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isepf=55xjt9pflsi - MPS2017-1.zip (264.15 MiB) http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isepf=ak4v31bzu4p Also, they left this message for you: Hi Bruce,
Re: [Freesurfer] Cannot run unpacksdcmdir on buckner_data/014-anon
Hi Doug, I ran the command you suggested and it appears to run without any errors or warnings. *OUTPUT: * anders@debian:~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon$ mri_convert 001.dcm deleteme.mgh mri_convert 001.dcm deleteme.mgh $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from 001.dcm... Getting Series No Scanning Directory INFO: Found 132 files in /home/anders/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon INFO: Scanning for Series Number 14 INFO: found 128 files in series INFO: loading series header info. INFO: sorting. RunNo = 13 INFO: (256 256 128), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix - 0.993 -0.117 0.033 1.187; 0.122 0.973 -0.197 -0.637; -0.009 0.200 0.980 5.207; 0.000 0.000 0.000 1.000; FileName /home/anders/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon/001.dcm Identification NumarisVersyngo MR 2004V 4VB11A ScannerModel Avanto PatientName anon Date and time StudyDate StudyTime 00 SeriesTime00 AcqTime 00 Acquisition parameters PulseSeq *tfl3d1_ns Protocol anon PhEncDir ROW EchoNo0 FlipAngle 7 EchoTime 3.26 InversionTime 1000 RepetitionTime2730 PhEncFOV 256 ReadoutFOV256 Image information RunNo 13 SeriesNo 14 ImageNo 1 NImageRows256 NImageCols256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 68.8536 138.9441 135.4929 VolRes 1. 1. 1.3300 VolDim256 256 128 Vc 0.1217 -0.9924 -0.0169 Vr 0.0065 0.0178 -0.9998 Vs -0.9925 -0.1216 -0.0086 VolCenter 0.7783 3.8396 4.6268 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=2730.00, TE=3.26, TI=1000.00, flip angle=7.00 i_ras = (0.121728, -0.99242, -0.0168585) j_ras = (0.00647436, 0.0177783, -0.999821) k_ras = (-0.992542, -0.121597, -0.008589) writing to deleteme.mgh... * *As far as I can tell, the Avanto is a Siemens model, which does not explain why unpacksdcmdir does not work, since unpacksdcmdir can find the slice with -scanonly but cannot unpack it. Any other ideas? Venlig hilsen | Kind regards Anders Dreisig Olsen anders.d.ol...@gmail.com mailto:anders.d.ol...@gmail.com On 07-01-2014 01:09, Douglas N Greve wrote: Not sure. Try running mri_convert 001.dcm deleteme.mgh if it fails, capture the screen output and send it to the list doug On 01/06/2014 06:31 PM, Anders Olsen wrote: Hello FreeSurfer team. I am currently trying to learn the general usage of FreeSurfer and have run into problems with unpacking DICOM files. When I run: unpacksdcmdir -src ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon -targ ~/fs_subjects/014-anon -scanonly ~/fs_subjects/014-anon/scan.info It completes and gives me the following output: 14anon ok 256 256 128 001.dcm I then try to unpack slice number 14 by running: unpacksdcmdir -src ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon -targ ~/fs_subjects/014-anon -fsfast -run 14 bold nii f.nii And it gives me the message: ERROR: reading ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon/001.dcm tag 28 30 I have done md5sum buckner_data-tutorial_subjs.tar.gz and got the hash: 14618f42ffa6b21d5714f37e159357c4 which matches the md5sum in ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.md5sum.txt Am I doing something wrong or is there a problem with the dcm files in the test data? -- Venlig hilsen | Kind regards Anders Dreisig Olsen anders.d.ol...@gmail.com mailto:anders.d.ol...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance
[Freesurfer] seeking a post-doc (fwd)
FYI Dear Colleagues, I hope this finds you well! I wanted to pass along an ad for a post-doc position on a motion correction project. We're having a tough time finding someone with both a strong interest in clinical autism research and technical sophistication with data analysis. Please pass this around and let me know if you can think of anyone or if you have suggestions on where to advertise. We did advertise at SFN. The position is available immediately. Thanks for your consideration and best wishes for a happy new year, Dara Dara S. Manoach, Ph.D. Psychiatric Neuroimaging and Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown Navy Yard 149 13th Street, Room 1.111 Charlestown, MA 02129 email: d...@nmr.mgh.harvard.edu phone: 617-724-6148 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] reconall error.
Hi Rashmi how did you create this dataset? The non-black background is probably going to cause trouble. Is it an mp2rage or something similar? Could you try replacing the background value (386.997) with 0 and see if that helps. If there are really big defects the topology fixer will take forever, and probably won't generate the correct solution anyway cheers Bruce On Tue, 7 Jan 2014, Rashmi Singh wrote: Hello FreeSurfer experts, I am having problem with running reconall. I am using version 5.1. Attached is data set on which I ran reconall. Because I was getting tailrace failure I ran it with –notal-check flag( the run with -use–mritotal flag failed too, so I used the –notal check flag ) Recon all ran OK, but its has got stuck at a point (topology detection stage) and its not moving forward (my terminal shows that its still running) May you please help me troubleshoot this issue. Thanks, Rashmi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] absolute value of effect size
Hi, I have two related questions. I have two conditions (e.g. C1 and C2) and I want to generate a map that shows all voxels that can differentiate C1 from C2 *irrespective* of whether C1C2 or C1C2. I think it can be done easily by: mris_calc -o sig.nii abs_sig.nii abs If I am right, then: 1) Can I apply the same command to ces.nii file to have the absolute value of the effect size (i.e. abs(C1-C2 effect size)) or should I consider other factors? 2) Do I need to apply the same routine to cesvar? Thanks -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] tksurfer display
Hi, Is there any way in tksurfer GUI display, that I can set a NVtxs threshold to get rid of regions (that came up significant after monte carlo simulation) which have NVtxs less than my input threshold. For eg. In my table below, I don't want postcentral label to appear in my tksurfer view (as I only want to see labels with more than 300 NVtxs). Can I get that label out from my brain pictures? # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWPCWPLow CWPHi NVtxs Annot 13.048 133418 89.23 52.8 -12.9 32.0 0.00020 0.0 0.00040 186 postcentral 22.938 109465989.46 36.0 17.2 31.1 0.00020 0.0 0.00040 1066 caudalmiddlefrontal Thanks, -Siddharth ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tksurfer display
You can run mri_annotation2label on the annotation to break it up into labels, then run mris_label2annot using only the label(s) you want doug On 01/07/2014 04:05 PM, Ray, Siddharth wrote: Hi, Is there any way in tksurfer GUI display, that I can set a NVtxs threshold to get rid of regions (that came up significant after monte carlo simulation) which have NVtxs less than my input threshold. For eg. In my table below, I don’t want postcentral label to appear in my tksurfer view (as I only want to see labels with more than 300 NVtxs). Can I get that label out from my brain pictures? # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 3.048 133418 89.23 52.8 -12.9 32.0 0.00020 0.0 0.00040 186 postcentral 2 2.938 109465 989.46 36.0 17.2 31.1 0.00020 0.0 0.00040 1066 caudalmiddlefrontal Thanks, -Siddharth ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Freesurfer templates for cross-ethnicity comparisons
Hi Bruce, I've been using Freesurfer to compare subcortical volumes and cortical thickness between Caucasian and Chinese controls. There are some significant findings, but the question of whether or not these may be biased due to the template has been raised (the assumption being that the majority of subjects used in the template are Caucasian). Is it possible to reduce the weight of the atlas during normalisation (or some other method to address the issue)? I would greatly appreciate your thoughts on this. Cheers, Linda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer templates for cross-ethnicity comparisons
Hi Linda I actually don't know the ethnicity of the subjects in our atlas. I wouldn't expect it to be an issue for folding patterns, but it is possible. You could build your own atlas and redo the analyses if you want to see if that changes things. I'll cc Mike Chee who I think has looked at this question as well. cheers Bruce On Tue, 7 Jan 2014, Linda Zhang wrote: Hi Bruce, I've been using Freesurfer to compare subcortical volumes and cortical thickness between Caucasian and Chinese controls. There are some significant findings, but the question of whether or not these may be biased due to the template has been raised (the assumption being that the majority of subjects used in the template are Caucasian). Is it possible to reduce the weight of the atlas during normalisation (or some other method to address the issue)? I would greatly appreciate your thoughts on this. Cheers, Linda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
