Hi Doug,

Thank you for your response! I am still a bit confused about the vol2surf command. I have a volumetric mask with voxels of interest based on a VBM analysis in SPM. I would like to extract the cortical thickness measurements based on these voxels. I am not clear what specifications I need to include when using vol2surf. For example, what do I use as my registration matrix?

Thank you for your help! Ola

Ola Ozranov-Palchik M.S. Research Coordinator, Gaab Lab Laboratories of Cognitive Neuroscience Children's Hospital Boston 1 Autumn Street, Mailbox # 713 Boston, MA 02115 olga.ozranov@childrens.harvard.edu phone: (617) 334-5046 main lab: (617) 355-0400 fax: (617) 730-0518 http://www.childrenshospital.org/research/gaablab

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, June 04, 2013 1:48 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] SPM ROI to Cortical Thickness

Make sure that your SPM volume is registered to the anatomical, then use mri_vol2surf to map the volume to the surface, then mri_segstats to extract the mean of the thickness

doug

On 06/04/2013 01:45 PM, Ozranov-Palchik, Ola wrote:

main lab: (617) 355-0400

Dear FreeSurfer Experts,

I was wondering if anyone can advise on the best way to use an ROI mask created in SPM (XjView) to extract cortical thickness values in freesurfer.

Thank you in advance for your help!

Ola

Ola Ozranov-Palchik M.S. Research Coordinator, Gaab Lab Laboratories of Cognitive Neuroscience

Children's Hospital Boston 1 Autumn Street, Mailbox # 713 Boston, MA 02115 olga.ozranov@childrens.harvard.edu mailto:olga.ozranov@childrens.harvard.edu phone: (617) 334-5046 main lab: (617) 355-0400 fax: (617) 730-0518 http://www.childrenshospital.org/research/gaablab

MNI space.

On Jun 5, 2013, at 11:14 AM, Douglas N Greve wrote:

what space is your VBM map in? doug

On 06/05/2013 11:06 AM, Ozranov-Palchik, Ola wrote: Hi Doug,

Thank you for your response! I am still a bit confused about the vol2surf command. I have a volumetric mask with voxels of interest based on a VBM analysis in SPM. I would like to extract the cortical thickness measurements based on these voxels. I am not clear what specifications I need to include when using vol2surf. For example, what do I use as my registration matrix?

Thank you for your help! Ola

Ola Ozranov-Palchik M.S. Research Coordinator, Gaab Lab Laboratories of Cognitive Neuroscience Children's Hospital Boston 1 Autumn Street, Mailbox # 713 Boston, MA 02115 olga.ozranov@childrens.harvard.edumailto:olga.ozranov@childrens.harvard.edu phone: (617) 334-5046 main lab: (617) 355-0400 fax: (617) 730-0518 http://www.childrenshospital.org/research/gaablab

-----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 Douglas N Greve Sent: Tuesday, June 04, 2013 1:48 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] SPM ROI to Cortical Thickness

Make sure that your SPM volume is registered to the anatomical, then use mri_vol2surf to map the volume to the surface, then mri_segstats to extract the mean of the thickness

doug

On 06/04/2013 01:45 PM, Ozranov-Palchik, Ola wrote: main lab: (617) 355-0400 Dear FreeSurfer Experts,

I was wondering if anyone can advise on the best way to use an ROI mask created in SPM (XjView) to extract cortical thickness values in freesurfer.

Thank you in advance for your help!

Ola

Ola Ozranov-Palchik M.S. Research Coordinator, Gaab Lab Laboratories of Cognitive Neuroscience

Children's Hospital Boston 1 Autumn Street, Mailbox # 713 Boston, MA 02115 olga.ozranov@childrens.harvard.edumailto:olga.ozranov@childrens.harvard.edu mailto:olga.ozranov@childrens.harvard.edu phone: (617) 334-5046 main lab: (617) 355-0400 fax: (617) 730-0518 http://www.childrenshospital.org/research/gaablab

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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.

Ola Ozranov-Palchik, M.S. Research Coordinator, Gaab Lab Laboratories of Cognitive Neuroscience Children's Hospital Boston 1 Autumn Street, Mailbox # 713 Boston, MA 02115 Ola.Ozranov-Palchik@tch.harvard.edumailto:olga.ozranov@childrens.harvard.edu phone: (617) 334-5046 main lab: (617) 355-0400 fax: (617) 730-0518 http://www.childrenshospital.org/research/gaablab

Hi Doug,

Thank you, again! I decided to try to use the Talairach coordinates from my analysis for ROI extraction. I created an average subject and preprocessed the data (mris_preproc). I obtained the vertex index based on the coordinates from the average subject. Any ideas on how I can now find the corresponding vertices in all my subjects?

Thanks very much! Ola

Hi Doug,

Thanks for the response. I'm still a bit confused.

Let's just say that I have a vertex index that I determined on the surface of my FS average surface (created by 'make_average_subject'). Now I simply want to find the corresponding vertex index on all the source subjects.

How can I do just this, i.e. map a single vertex from the average surface to all the subjects?

Thanks very much! Ola

Hi FreeSurfers,

I ran the longitudinal processing pipeline on my subjects, FS 5.0. Following the tutorial, first independently, then base, then long etc. Everything works well, no problems there.

Out of curiosity I compared the asegstats & aparcstats within subject at baseline (i.e. The same timepoint): so the independent fsid vs the same_fsid.long.same_fsid_template, and there are (large) differences between all volumes/thicknesses. The independent measures are in almost all brain areas larger compared to those derived from the longi-stream. Except for the IC, which is completely the same, but of course, this measure is based on the Buckner method and calculated differently.

Overall this seems a bit strange to me, because I believe there shouldn't be differences within subject on the same time-point. Is this the result of the within-subject template use for the longitudinal data or is something else going wrong, or is this normal?

Many thanks!

Cheers, Cédric

------------------------------------------------------------ P.C.M.P. Koolschijn (Cédric), PhD Dutch Autism & ADHD Research Center Brain and Cognition Amsterdam, The Netherlands E P.C.M.P.Koolschijn@uva.nlmailto:P.C.M.P.Koolschijn@uva.nl W http://www.dutcharc.nl

Hi Martin,

Thanks for your fast response. Apologies for the second email, I forgot to include the mailinglist.

It makes sense that in the longi-stream results should be more reliable.

However, it worries me if I see segmentation differences up to 500%, for example amygdala volume going from 1475 to 503 Left and 1595 to 281 for Right, independent vs longitudinal stream respectively. In the current study we had a cross-sectional exploration study, followed by a longitudinal validation study (so two different samples). The above worries me if we want to compare the cross-sectional results with the longitudinal results, as the differences between independent and longitudinal are in a linear fashion.

Any thoughts on this?

Cheers, Cédric

From: Martin Reuter <mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu> Date: Tuesday, June 25, 2013 8:00 PM To: Cédric Koolschijn <P.C.M.P.Koolschijn@uva.nlmailto:P.C.M.P.Koolschijn@uva.nl> Cc: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing

Hi Cedric,

this is as expected, the data changes when using the longitudinal stream (it will become more reliable, removing some of the variance you get in the independent processing). Becuase of the different processing approaches, the results from independent processing (cross) and long will not be directly comparable.

Cheers, Martin

On 06/25/2013 04:02 AM, Koolschijn, Cédric wrote: Hi FreeSurfers,

I ran the longitudinal processing pipeline on my subjects, FS 5.0. Following the tutorial, first independently, then base, then long etc. Everything works well, no problems there.

Out of curiosity I compared the asegstats & aparcstats within subject at baseline (i.e. The same timepoint): so the independent fsid vs the same_fsid.long.same_fsid_template, and there are (large) differences between all volumes/thicknesses. The independent measures are in almost all brain areas larger compared to those derived from the longi-stream. Except for the IC, which is completely the same, but of course, this measure is based on the Buckner method and calculated differently.

Overall this seems a bit strange to me, because I believe there shouldn't be differences within subject on the same time-point. Is this the result of the within-subject template use for the longitudinal data or is something else going wrong, or is this normal?

Many thanks!

Cheers, Cédric

------------------------------------------------------------ P.C.M.P. Koolschijn (Cédric), PhD Dutch Autism & ADHD Research Center Brain and Cognition Amsterdam, The Netherlands E P.C.M.P.Koolschijn@uva.nlmailto:P.C.M.P.Koolschijn@uva.nl W http://www.dutcharc.nl

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://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: mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu reuter@mit.edumailto:reuter@mit.edu Web : http://reuter.mit.edu

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.

You should take the better of the two images (the one without motion artifacts).

Cheers, Martin

On 06/26/2013 11:06 AM, MCLAREN, Donald wrote:

This raises an interesting question.

Given that the longitudinal process is more reliable, if we collect 2 scans on the same day, should we average those scans and then submit to Freesurfer or apply Freesurfer first and then create an average of the metrics from the longitudinal pipeline?

Best Regards, Donald McLaren

D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren http://www.martinos.org/%7Emclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

On Tue, Jun 25, 2013 at 2:00 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu> wrote:

Hi Cedric,

this is as expected, the data changes when using the longitudinal
stream (it will become more reliable, removing some of the
variance you get in the independent processing). Becuase of the
different processing approaches, the results from independent
processing (cross) and long will not be directly comparable.

Cheers, Martin



On 06/25/2013 04:02 AM, Koolschijn, Cédric wrote:

...

Hi FreeSurfers,

I ran the longitudinal processing pipeline on my subjects, FS 5.0.
Following the tutorial, first independently, then base, then long
etc. Everything works well,  no problems there.

Out of curiosity I compared the asegstats & aparcstats within
subject at baseline (i.e. The same timepoint): so the independent
fsid vs the same_fsid.long.same_fsid_template, and there are
(large) differences between all volumes/thicknesses. The
independent measures are in almost all brain areas larger
compared to those derived from the longi-stream. Except for the
IC, which is completely the same, but of course, this measure is
based on the Buckner method and calculated differently.

Overall this seems a bit strange to me, because I believe there
shouldn't be differences within subject on the same time-point.
Is this the result of the within-subject template use for the
longitudinal data or is something else going wrong, or is this
normal?

Many thanks!

Cheers,
Cédric

------------------------------------------------------------
P.C.M.P. Koolschijn (Cédric), PhD
Dutch Autism & ADHD Research Center
Brain and Cognition
Amsterdam, The Netherlands
/E /P.C.M.P.Koolschijn@uva.nl <mailto:P.C.M.P.Koolschijn@uva.nl>
/W /http://www.dutcharc.nl



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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  <tel:%2B1-617-724-5652>
Email:
    mreuter@nmr.mgh.harvard.edu  <mailto:mreuter@nmr.mgh.harvard.edu>
    reuter@mit.edu  <mailto:reuter@mit.edu>
Web  :http://reuter.mit.edu  


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the e-mail
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