[Freesurfer] conversion from dicom to mgz
How do i convert dicom into mgz files. tried using recon-all what does subject id refer to and what is its significance. ___ 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] mri_tesselate: max vertices 1000000 exceeded
Thanks for your quick reply. It seems that we have some other problems now with the machine, but 'll let you know whether the new mri_tessellate works ;-). On Fri, Sep 6, 2013 at 5:16 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: here you go. Let us know if it works cheers Bruce On Fri, 6 Sep 2013, Martijn Steenwijk wrote: Dear all, I'm trying to process some high res data using the approach Lusebrink proposed, but I'm getting the following error in mri_tessellate: mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ mri_tessellate: max vertices 100 exceeded It seems that max number of faces and vertices is hardly defined in the code. Would it be possible to provide another compiled version (centos6_x86_64-stable-pub-5.**3.0) with these numbers doubled or so? Best regards, Martijn 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/**compliancelinehttp://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 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] version 2 FS
Dear SIr, I made some analysis based on FS v.2.0. Does the Deprecated version means that the results generated by FSv.2 can't be published??? ___ 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] recon-all for multiple subjects
Dear Sir, I'd like to know the command lines for running recon-all for multiple datasets. Can you please help me on that? I've tried using the following command lines cd /home/john/Anu (where I kept all the .nii files) for x in * do recon-all -i SZ*.nii -s $x -all done But this is not working ___ 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] version 2 FS
I really meant FS5.2.. Sorry for the lack of clarity of my prev. mail From: Anupa AV av.an...@yahoo.com To: Freesurfer freesurfer@nmr.mgh.harvard.edu; Bruce Fischl fis...@nmr.mgh.harvard.edu Sent: Saturday, September 7, 2013 3:14 PM Subject: version 2 FS Dear SIr, I made some analysis based on FS v.2.0. Does the Deprecated version means that the results generated by FSv.2 can't be published???___ 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] conversion from dicom to mgz
subject id is the identifier you pick for that subject. It is arbirtary but needs to be unique (at least in that SUBJECTS_DIR). recon-all will read dicom fine and create .mgz files from it. Try it and if it fails send us your full command line and screen output and we will tell you what was incorrect. cheers Bruce On Sat, 7 Sep 2013, swathy p.s wrote: How do i convert dicom into mgz files. tried using recon-all what does subject id refer to and what is its significance. ___ 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] version 2 FS
Hi Anupa it means that for some acquisition types the pial surfaces in 5.2 had substantial errors. We recommend rerunning with 5.3. Note that this should just involve compute time as all manual interventions will be retained cheers Bruce On Sat, 7 Sep 2013, Anupa AV wrote: Dear SIr, I made some analysis based on FS v.2.0. Does the Deprecated version means that the results generated by FSv.2 can't be published??? ___ 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] recon-all for multiple subjects
Hi Anupa
in general recon-all only processes a single dataset at a time. You can run
multiple versions of recon-all if you have the processors and memory to
support it. Something like:
foreach x ( *)
recon-all -i SZ.${x}.nii -s $x -all
end
assuming that you had already converted your dicom files to nifti and named
them accordingly.
You will need 4G of ram and a cpu for each process to make this worthwhile
I think
cheers
Bruce
On Sat, 7 Sep 2013, Anupa AV wrote:
Dear Sir,
I'd like to know the command lines for running recon-all for multiple
datasets.
Can you please help me on that?
I've tried using the following command lines
cd /home/john/Anu (where I kept all the .nii files)
for x in *
do
recon-all -i SZ*.nii -s $x -all
done
But this is not working
___
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Re: [Freesurfer] recon-all for multiple subjects
The problem here is that SZ*.nii presumably refers to a list of files due to shell expansion. I don't know how recon-all handles that (e.g. if it will take only the first file in the list, or all files), but that command probably won't do what you want it to. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anupa AV [av.an...@yahoo.com] Sent: Saturday, September 07, 2013 5:56 AM To: KOOL; Freesurfer Subject: [Freesurfer] recon-all for multiple subjects Dear Sir, I'd like to know the command lines for running recon-all for multiple datasets. Can you please help me on that? I've tried using the following command lines cd /home/john/Anu (where I kept all the .nii files) for x in * do recon-all -i SZ*.nii -s $x -all done But this is not working ___ 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] recon-all for multiple subjects
it won't handle it. If you gave it multiple inputs each with it's own -i it would assume that they are different images of the same subject and perform motion correction and averaging. I don't think that is the case here - you want to give each instance of recon-all a single nifti volume as input (unless you acquired multiple T1-weighted images/session) cheers Bruce On Sat, 7 Sep 2013, Watson, Christopher wrote: The problem here is that SZ*.nii presumably refers to a list of files due to shell expansion. I don't know how recon-all handles that (e.g. if it will take only the first file in the list, or all files), but that command probably won't do what you want it to. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anupa AV [av.an...@yahoo.com] Sent: Saturday, September 07, 2013 5:56 AM To: KOOL; Freesurfer Subject: [Freesurfer] recon-all for multiple subjects Dear Sir, I'd like to know the command lines for running recon-all for multiple datasets. Can you please help me on that? I've tried using the following command lines cd /home/john/Anu (where I kept all the .nii files) for x in * do recon-all -i SZ*.nii -s $x -all done But this is not working ___ 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 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] version 2 FS
Note that this does not apply to HCP-style FreeSurfer runs or the HCP released data. Peace, Matt. On 9/7/13 8:26 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Anupa it means that for some acquisition types the pial surfaces in 5.2 had substantial errors. We recommend rerunning with 5.3. Note that this should just involve compute time as all manual interventions will be retained cheers Bruce On Sat, 7 Sep 2013, Anupa AV wrote: Dear SIr, I made some analysis based on FS v.2.0. Does the Deprecated version means that the results generated by FSv.2 can't be published??? ___ 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] recon-all for multiple subjects
Anupa, If you want to run several subjects at the same time just open different command windows. On each you can run a recon all. You can also run a list of recon on each window. Just put the commands in a text file, name it something like i.e. group1.sh and run the command sh group1.sh. Each subject will be done in sequence and each command window can have its own sequence. If you add the appropriate linux command you can also receive an email when the list of subjects is done. Hope helps 2013/9/7 Bruce Fischl fis...@nmr.mgh.harvard.edu it won't handle it. If you gave it multiple inputs each with it's own -i it would assume that they are different images of the same subject and perform motion correction and averaging. I don't think that is the case here - you want to give each instance of recon-all a single nifti volume as input (unless you acquired multiple T1-weighted images/session) cheers Bruce On Sat, 7 Sep 2013, Watson, Christopher wrote: The problem here is that SZ*.nii presumably refers to a list of files due to shell expansion. I don't know how recon-all handles that (e.g. if it will take only the first file in the list, or all files), but that command probably won't do what you want it to. From: freesurfer-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anupa AV [ av.an...@yahoo.com] Sent: Saturday, September 07, 2013 5:56 AM To: KOOL; Freesurfer Subject: [Freesurfer] recon-all for multiple subjects Dear Sir, I'd like to know the command lines for running recon-all for multiple datasets. Can you please help me on that? I've tried using the following command lines cd /home/john/Anu (where I kept all the .nii files) for x in * do recon-all -i SZ*.nii -s $x -all done But this is not working ___ 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 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 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] cluster threshold
Hi FreeSurfer Experts, On this page (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons), it says: In particular, thresholds of 1.3, 2, 2.3, 3, 3.3 and 4, corresponding to p-values of 0.05, 0.01, 0.005, 0.001, 0.0005 and 0.0001, which are common thresholds. I am wondering how these thresholds were computed. In my own computation, I found z-value to be the following, but neither one-sided nor two-sided matches the thresholds of 1.3, …, 4 as shown above? one-sided: p-value=0.0500, z-value=1.6 p-value=0.0100, z-value=2.3 p-value=0.0050, z-value=2.6 p-value=0.0010, z-value=3.1 p-value=0.0005, z-value=3.3 p-value=0.0001, z-value=3.7 two-sided: p-value=0.0500, z-value=2.0 p-value=0.0100, z-value=2.6 p-value=0.0050, z-value=2.8 p-value=0.0010, z-value=3.3 p-value=0.0005, z-value=3.5 p-value=0.0001, z-value=3.9 Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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] conversion from dicom to mgz
mri_convert dicomfile file.mgz where dicomfile is a single file from the series (it will find the rest) On 9/7/13 3:28 AM, swathy p.s wrote: How do i convert dicom into mgz files. tried using recon-all what does subject id refer to and what is its significance. ___ 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 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.
