Hi, I'm wondering if it's okay to run some of the analyses within one study on v.5.3 and the other hippocampal analyses on 6.0? Or do you recommend us starting over for the analyses we've already done in 5.3 for that study?
Thank you! Batool
Hi, Can anyone comment on my question below? I think the FAQ page mentions that the same version should be used to process all cases within a dataset, but my question is whether I can have the same dataset used for two different versions for separate analyses? This is considering that I've already processed all my data with 5.3, but am interested in getting hippocampal subfields through 6.0.
Thanks so much! Batool ________________________________ From: Rizvi, Batool Sent: Wednesday, January 25, 2017 12:54 PM To: freesurfer@nmr.mgh.harvard.edu Subject: freesurfer 6.0 with some of the analyses
Hi, I'm wondering if it's okay to run some of the analyses within one study on v.5.3 and the other hippocampal analyses on 6.0? Or do you recommend us starting over for the analyses we've already done in 5.3 for that study?
Thank you! Batool
I believe Dr. Iglesias previous responses on this exact question have been, "yes it's possible, but your results may be harder to reproduce" e.g. If someone wanted to replicate your study they may have a harder time having to download 2 different versions of freesurfer to achieve comparable results with your study.
I think the general consensus is "how many subjects do you have?" -- if it's less than 50, you may want to just rerun v6 on your subjects as it should preserve the edits -- but it's recommended you still open them up and double check.
-Adam
On Thu, Jan 26, 2017 at 8:37 AM Rizvi, Batool br2499@cumc.columbia.edu wrote:
Hi,
Can anyone comment on my question below?
I think the FAQ page mentions that the same version should be used to process all cases within a dataset, but my question is whether I can have the same dataset used for two different versions for separate analyses? This is considering that I've already
processed all my data with 5.3, but am interested in getting hippocampal subfields through 6.0.
Thanks so much!
Batool
*From:* Rizvi, Batool
*Sent:* Wednesday, January 25, 2017 12:54 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* freesurfer 6.0 with some of the analyses
Hi,
I'm wondering if it's okay to run some of the analyses within one study on v.5.3 and the other hippocampal analyses on 6.0?
Or do you recommend us starting over for the analyses we've already done in 5.3 for that study?
Thank you!
Batool
Freesurfer mailing list
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contains patient information, please contact the Partners Compliance HelpLine at
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Dear Batool, Sorry for missing your message. And dear Adam: Thanks for covering me! That’s exactly my standard answer to that question ;-)
Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
On 26 Jan 2017, at 15:55, Adam Martersteck <acmarter@gmail.commailto:acmarter@gmail.com> wrote:
I believe Dr. Iglesias previous responses on this exact question have been, "yes it's possible, but your results may be harder to reproduce" e.g. If someone wanted to replicate your study they may have a harder time having to download 2 different versions of freesurfer to achieve comparable results with your study.
I think the general consensus is "how many subjects do you have?" -- if it's less than 50, you may want to just rerun v6 on your subjects as it should preserve the edits -- but it's recommended you still open them up and double check.
-Adam
On Thu, Jan 26, 2017 at 8:37 AM Rizvi, Batool <br2499@cumc.columbia.edumailto:br2499@cumc.columbia.edu> wrote:
Hi,
Can anyone comment on my question below?
I think the FAQ page mentions that the same version should be used to process all cases within a dataset, but my question is whether I can have the same dataset used for two different versions for separate analyses? This is considering that I've already
processed all my data with 5.3, but am interested in getting hippocampal subfields through 6.0.
Thanks so much!
Batool
________________________________
From: Rizvi, Batool
Sent: Wednesday, January 25, 2017 12:54 PM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: freesurfer 6.0 with some of the analyses
Hi,
I'm wondering if it's okay to run some of the analyses within one study on v.5.3 and the other hippocampal analyses on 6.0?
Or do you recommend us starting over for the analyses we've already done in 5.3 for that study?
Thank you!
Batool
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto: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
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dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
Thanks for your responses!
Sorry for the naive question, but I'm wondering which commands I'd use to re-process all the data from 5.3. Can I run recon-all -all, and it will go through all the steps that it would if I ran it from the start? Or would it skip certain steps if it finds certain files existing already. I'm pretty sure the former is true, but just wanted to confirm.
Thanks again!
Batool ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.iglesias@ucl.ac.uk] Sent: Thursday, January 26, 2017 11:01 AM To: Freesurfer support list Subject: Re: [Freesurfer] freesurfer 6.0 with some of the analyses
Dear Batool, Sorry for missing your message. And dear Adam: Thanks for covering me! That’s exactly my standard answer to that question ;-)
Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
On 26 Jan 2017, at 15:55, Adam Martersteck <acmarter@gmail.commailto:acmarter@gmail.com> wrote:
I believe Dr. Iglesias previous responses on this exact question have been, "yes it's possible, but your results may be harder to reproduce" e.g. If someone wanted to replicate your study they may have a harder time having to download 2 different versions of freesurfer to achieve comparable results with your study.
I think the general consensus is "how many subjects do you have?" -- if it's less than 50, you may want to just rerun v6 on your subjects as it should preserve the edits -- but it's recommended you still open them up and double check.
-Adam
On Thu, Jan 26, 2017 at 8:37 AM Rizvi, Batool <br2499@cumc.columbia.edumailto:br2499@cumc.columbia.edu> wrote:
Hi,
Can anyone comment on my question below?
I think the FAQ page mentions that the same version should be used to process all cases within a dataset, but my question is whether I can have the same dataset used for two different versions for separate analyses? This is considering that I've already
processed all my data with 5.3, but am interested in getting hippocampal subfields through 6.0.
Thanks so much!
Batool
________________________________
From: Rizvi, Batool
Sent: Wednesday, January 25, 2017 12:54 PM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: freesurfer 6.0 with some of the analyses
Hi,
I'm wondering if it's okay to run some of the analyses within one study on v.5.3 and the other hippocampal analyses on 6.0?
Or do you recommend us starting over for the analyses we've already done in 5.3 for that study?
Thank you!
Batool
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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You are correct that the former is true.
Run recon-all -all on your existing subject directories after moving them to a new v6 directory (with the new fsaverage, etc.) -- it will rerun all the commands and use your brainmask.mgz deleted voxels, and your wm.mgz 255 voxels to correct the surfaces.
You will still need to open your subjects up in tkmedit or freeview and inspect the surfaces for errors.
On Fri, Jan 27, 2017 at 11:13 AM Rizvi, Batool br2499@cumc.columbia.edu wrote:
Thanks for your responses!
Sorry for the naive question, but I'm wondering which commands I'd use to re-process all the data from 5.3. Can I run recon-all -all, and it will go through all the steps that it would if I ran it from the start? Or would it skip certain steps if it finds
certain files existing already. I'm pretty sure the former is true, but just wanted to confirm.
Thanks again!
Batool
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.iglesias@ucl.ac.uk]
*Sent:* Thursday, January 26, 2017 11:01 AM
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] freesurfer 6.0 with some of the analyses
Dear Batool,
Sorry for missing your message.
And dear Adam:
Thanks for covering me! That’s exactly my standard answer to that question ;-)
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
On 26 Jan 2017, at 15:55, Adam Martersteck acmarter@gmail.com wrote:
I believe Dr. Iglesias previous responses on this exact question have been, "yes it's possible, but your results may be harder to
reproduce"
e.g. If someone wanted to replicate your study they may have a harder time having to download 2 different versions of freesurfer
to achieve comparable results with your study.
I think the general consensus is "how many subjects do you have?" -- if it's less than 50, you may want to just rerun
v6 on your subjects as it should preserve the edits -- but it's recommended you still open them up and double check.
-Adam
On Thu, Jan 26, 2017 at 8:37 AM Rizvi, Batool br2499@cumc.columbia.edu wrote:
Hi,
Can anyone comment on my question below?
I think the FAQ page mentions that the same version should be used to process all cases within a dataset, but my question is whether I can have the same dataset used for two different versions for separate analyses? This is considering
that I've already
processed all my data with 5.3, but am interested in getting hippocampal subfields through 6.0.
Thanks so much!
Batool
*From:* Rizvi, Batool
*Sent:* Wednesday, January 25, 2017 12:54 PM
*To:*
freesurfer@nmr.mgh.harvard.edu
*Subject:* freesurfer 6.0 with some of the analyses
Hi,
I'm wondering if it's okay to run some of the analyses within one study on v.5.3 and
the other hippocampal analyses on 6.0?
Or do you recommend us starting over for the analyses we've already done in 5.3 for that study?
Thank you!
Batool
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
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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
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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@nmr.mgh.harvard.edu
-
Adam Martersteck -
Iglesias Gonzalez, Eugenio -
Rizvi, Batool