[Freesurfer] Freesurfer-Error message
Hi, While running the following command: recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre -subjid test2 I keep seeing the following error: ... corRead(): can't open file /media/sf_freesurferstudys/raw/raw_scr/T1pre/COR-.info $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /media/sf_freesurferstudys/raw/raw_scr/T1pre... Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s test2 exited with ERRORS at Fri Aug 31 04:20:28 EDT 2012 My image files, in dcm format, are at /media/sf_freesurferstudys/raw/raw_scr/T1pre : /media/sf_freesurferstudys/raw/raw_scr/T1pre ls Image1 Image00010 Image00019 Image00028 Image00037 Image00046 Image2 Image00011 Image00020 Image00029 Image00038 Image00047 Image3 Image00012 Image00021 Image00030 Image00039 Image00048 Image4 Image00013 Image00022 Image00031 Image00040 Image00049 Image5 Image00014 Image00023 Image00032 Image00041 Image00050 Image6 Image00015 Image00024 Image00033 Image00042 Image7 Image00016 Image00025 Image00034 Image00043 Image8 Image00017 Image00026 Image00035 Image00044 Image9 Image00018 Image00027 Image00036 Image00045 Many thanks for your help. chikku ___ 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 tutorial data
Dear sirs and madames, unfortunately I wasn't able to download the tutorial data for freesurfer. The download interrupted at 2 GB within the bruckner_data_tutorial_subjs.tar.gz I already did the recon_all process for 90 brains and wanted to improve my skills for the corrections. Is there any advise you can give to get the tutorial data? Best regards, Dix Meiberth (B.Sc. Neurowissenschaften) Funktionelle Bildgebung Klinik und Poliklinik für Psychiatrie und Psychotherapie Universitätsklinikum Bonn Sigmund-Freud-Strasse 25 53105 Bonn Tel. 0228-287-16366 dix.meibe...@ukb.uni-bonn.de ___ 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] creating a skull
Also, is there a way to create a skull from a CT scan? From: Borzello, Mia Sent: Friday, August 31, 2012 12:17 PM To: freesurfer Subject: RE: [Freesurfer] creating a skull I've been referred to the following link on the freesurfer site to handle this, but is this still current (i.e. is linux still needed to do this?): http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004679.html thanks, m From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu] Sent: Friday, August 31, 2012 10:29 AM To: Borzello, Mia Cc: freesurfer Subject: Re: [Freesurfer] creating a skull Hi, You need to add an extension onto the file name, something like brain.mgz or brain.nii. The extension will tell it what format to save the output in. -Louis On Fri, 31 Aug 2012, Borzello, Mia wrote: Hi freesurfer family, I am trying to create the inner skull boundary and ran: mri_watershed -atlas - surf -useSRAS mri.nii brain However, after it finished running it said it was saving brain, but brain was an unknown file type. Am i supposed to specify that somewhere? Thanks in advance, m ___ 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] creating a skull
Hi Mia you would need to mess around with watershed and such, it might work or might not. cheers Bruce On Mon, 3 Sep 2012, Borzello, Mia wrote: Also, is there a way to create a skull from a CT scan? From: Borzello, Mia Sent: Friday, August 31, 2012 12:17 PM To: freesurfer Subject: RE: [Freesurfer] creating a skull I've been referred to the following link on the freesurfer site to handle this, but is this still current (i.e. is linux still needed to do this?): http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004679.html thanks, m From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu] Sent: Friday, August 31, 2012 10:29 AM To: Borzello, Mia Cc: freesurfer Subject: Re: [Freesurfer] creating a skull Hi, You need to add an extension onto the file name, something like brain.mgz or brain.nii. The extension will tell it what format to save the output in. -Louis On Fri, 31 Aug 2012, Borzello, Mia wrote: Hi freesurfer family, I am trying to create the inner skull boundary and ran: mri_watershed -atlas - surf -useSRAS mri.nii brain However, after it finished running it said it was saving brain, but brain was an unknown file type. Am i supposed to specify that somewhere? Thanks in advance, m ___ 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 ___ 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-Error message
Hi Chikku you need to give it the path to an image file (any one will do) and it will figure out the other slices that makeup the same series. What is the resolution of your data? 50 slices isn't usually enough to cover the brain at high enough resolution to get good thickness results. cheers Bruce On Mon, 3 Sep 2012, Varghese Chikku wrote: Hi, While running the following command: recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre -subjid test2 I keep seeing the following error: ... corRead(): can't open file /media/sf_freesurferstudys/raw/raw_scr/T1pre/COR-.info $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /media/sf_freesurferstudys/raw/raw_scr/T1pre... Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s test2 exited with ERRORS at Fri Aug 31 04:20:28 EDT 2012 My image files, in dcm format, are at /media/sf_freesurferstudys/raw/raw_scr/T1pre : /media/sf_freesurferstudys/raw/raw_scr/T1pre ls Image1 Image00010 Image00019 Image00028 Image00037 Image00046 Image2 Image00011 Image00020 Image00029 Image00038 Image00047 Image3 Image00012 Image00021 Image00030 Image00039 Image00048 Image4 Image00013 Image00022 Image00031 Image00040 Image00049 Image5 Image00014 Image00023 Image00032 Image00041 Image00050 Image6 Image00015 Image00024 Image00033 Image00042 Image7 Image00016 Image00025 Image00034 Image00043 Image8 Image00017 Image00026 Image00035 Image00044 Image9 Image00018 Image00027 Image00036 Image00045 Many thanks for your help. chikku ___ 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] question about painting SPM results onto Freesurfer
Hi Karry painting is done by mri_vol2surf and you can use it to specify how you want the sampling to be done. We typically sample the volume halfway our from the gray/white boundary, or sometimes a bit lower to avoid vascular artifacts at the pial surface. That said, it is quite flexible and you can use it to sample however you wish (e.g. average over the bottom third of cortex, etc). When we sample we don't inspect the value, just grab it from the volume and assign it to the surface so if there are significant cluster that aren't intersected by the sampling band you specify they will not appear on the surface. cheers Bruce On Sun, 2 Sep 2012, keepmoon wrote: Hello everyone, I just read the information about paintig SPM results onto Freesurfer (http://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting). It shows how to painting SPM results from statistic step (ex. spmT.img) to surface space. I tested the procedure and it worked. But I don't understand what is displayed on Freesurfer surface. Are all the significant differences from SPM statistic results are displayed on this surface? or some part of t values are displayed (which part)? As cortical thickness displayed on surface, each thickness value is painted on each vertex. But here t-value image from SPM is volume image, how to paint it on surface? Someone could give a little detailed explaination?? Thanks in advance Karry ___ 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] question about painting SPM results onto Freesurfer
Hi Bruce, Thanks for your detailed explaination! I have one more question about it! Is it possible to get cluster size for being painted SPM results on freesure surface (like getting the cluster size of cortical thickness in QDEC )? Is there any command getting it? Any idea will be appreciated! Thanks! Karry On Mon, Sep 3, 2012 at 5:37 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Karry painting is done by mri_vol2surf and you can use it to specify how you want the sampling to be done. We typically sample the volume halfway our from the gray/white boundary, or sometimes a bit lower to avoid vascular artifacts at the pial surface. That said, it is quite flexible and you can use it to sample however you wish (e.g. average over the bottom third of cortex, etc). When we sample we don't inspect the value, just grab it from the volume and assign it to the surface so if there are significant cluster that aren't intersected by the sampling band you specify they will not appear on the surface. cheers Bruce On Sun, 2 Sep 2012, keepmoon wrote: Hello everyone, I just read the information about paintig SPM results onto Freesurfer (http://surfer.nmr.mgh.**harvard.edu/fswiki/SpmPaintinghttp://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting **). It shows how to painting SPM results from statistic step (ex. spmT.img) to surface space. I tested the procedure and it worked. But I don't understand what is displayed on Freesurfer surface. Are all the significant differences from SPM statistic results are displayed on this surface? or some part of t values are displayed (which part)? As cortical thickness displayed on surface, each thickness value is painted on each vertex. But here t-value image from SPM is volume image, how to paint it on surface? Someone could give a little detailed explaination?? Thanks in advance Karry 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.
Re: [Freesurfer] question about painting SPM results onto Freesurfer
you mean the size of the cluster on the surface? Yes, you can do that, but you'll need to wait for Doug's return for the details cheers Bruce On Mon, 3 Sep 2012, keepmoon wrote: Hi Bruce, Thanks for your detailed explaination! I have one more question about it! Is it possible to get cluster size for being painted SPM results on freesure surface (like getting the cluster size of cortical thickness in QDEC )? Is there any command getting it? Any idea will be appreciated! Thanks! Karry On Mon, Sep 3, 2012 at 5:37 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Karry painting is done by mri_vol2surf and you can use it to specify how you want the sampling to be done. We typically sample the volume halfway our from the gray/white boundary, or sometimes a bit lower to avoid vascular artifacts at the pial surface. That said, it is quite flexible and you can use it to sample however you wish (e.g. average over the bottom third of cortex, etc). When we sample we don't inspect the value, just grab it from the volume and assign it to the surface so if there are significant cluster that aren't intersected by the sampling band you specify they will not appear on the surface. cheers Bruce On Sun, 2 Sep 2012, keepmoon wrote: Hello everyone, I just read the information about paintig SPM results onto Freesurfer (http://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting). It shows how to painting SPM results from statistic step (ex. spmT.img) to surface space. I tested the procedure and it worked. But I don't understand what is displayed on Freesurfer surface. Are all the significant differences from SPM statistic results are displayed on this surface? or some part of t values are displayed (which part)? As cortical thickness displayed on surface, each thickness value is painted on each vertex. But here t-value image from SPM is volume image, how to paint it on surface? Someone could give a little detailed explaination?? Thanks in advance Karry 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.
Re: [Freesurfer] FDR Correction of NHP Surface Data
Hi Clark sorry, the end of the summer has been a period when things slip through the cracks. I think what you want is possible without a talairach or aseg, but it will need to wait for Doug to get back. Can you repost at the end of next week? Bruce On Thu, 30 Aug 2012, Clark Fisher wrote: Thanks Michael, I'll look into Nipy's FDR tools. I actually started this thread asking for help getting mri_surfcluster running for my situation (I have no talraich .xfm and no segmentation for my monkeys). The silence on that topic suggest that it might not be possible, or it's at least not known to possible. Thanks again everyone. -Clark On Aug 29, 2012, at 6:55 PM, Michael Waskom wrote: Hi Clark, If you're loading the data into Python anyway to use with PySurfer, Nipy seems to have some utilities to do an FDR correction (docs/source). I've never used these, but they look pretty straightforward. Also it looks like FDR is built into mri_surfcluster. Best, Michael On Wed, Aug 29, 2012 at 2:08 PM, Clark Fisher cfis...@mail.rockefeller.edu wrote: Hi Sebastian, I think you are right, both about tksurfer thresholding and the correct interpretation of FDR. As you point out though, there is some value in having maps that show how relatively well different points on the surface fit your model. At the very least, is there any way to automate the retrieving of the threshold that tksurfer provides? I'd still also be interested in some adjustment to the whole map, if there's a way to do that as well. I could probably find a way to do this in Matlab, but I trust the bug-squishing abilities of the freesurfer community more than I trust my own. -Clark On Aug 28, 2012, at 2:34 PM, Sebastian Moeller wrote: Hi Clark, On Aug 28, 2012, at 11:15 AM, Clark Fisher wrote: Hi Bruce, Thanks. I actually have used this function of tksurfer, but am looking for a way to save the corrected maps, so that they could be manipulated by other tools (for instance, viewed by PySurfer). Does it really correct the map? I thought all it does is figure out the corrected threshold. By the way, if I understand correctly, FDR maps should be considered to be binary, that is you really do not know which voxels might be false positives, so you should not interpret all voxels to be equally significant. Having said that, almost everybody I know still looks at the p-value spatial distribution when looking at those FDR thresholded maps? (then again, I do not know any statistician...) best Sebastian I recognize that this may not be an officially supported functionality, but is there some way to save the adjusted overlays from tksurfer, or create them in some other way? Best, Clark On Aug 28, 2012, at 1:58 PM, Bruce Fischl wrote: Hi Clark you shouldn't need either. Load your overlays then click the button to compute the FDR threshold in the tksurfer configure overlay interface. cheers Bruce On Tue, 28 Aug 2012, Clark Fisher wrote: Ok, maybe I'm making this question too intricate. Here's the short version: How can I FDR correct painted surface significance maps when I have no talraich .xfm file and no cortical segmentation? Thanks again, Clark Hi Freesurfers, I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: 1) I don't have any .xfm files for my monkeys, as I'm working in native space, and 2) Without segmentation, I don't have a good mask to use for the cortex only. My first attempts at work-arounds would be: 1)Try to create an identity .xfm file 2)Use the cortical ribbons from mris_volmask as a cortex mask Should these work? If so, how should I make an identity .xfm file? If not, is there another way to FDR correct my surface data? Thanks, Clark ___ 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
Re: [Freesurfer] cortical volume and ortical jacobian_whitematter
Hi Knut these are hard questions to answer. Volume is thickness x surface area, so the question is how reliable is surface area and what does a change in it mean? Where does the jacobian_whitematter measure come from? cheers Bruce On Thu, 30 Aug 2012, Knut J Bjuland wrote: Hi, I have looked into cortical surface volume and cortical jacobian_whitematter. Can I use these measure a in similar way as cortical thickness? Do jacobian_whitematter represent the whitematter thickness in the cortex? How reliable are cortical volumes compared to cortical thickness? Best regard Knut J ___ 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] how i can compute volume of a VOI
Hi Eustratios the label file is a simple text format that contains the number of voxels in the first line or two. Since our voxels are 1mm isotropic that will also correspond to the volume. You could create a volume and use mri_segstats, but this would be much easier. cheers Bruce On Fri, 31 Aug 2012, Eustratios Karavasilis wrote: Dear all, i am new Freesurfer user (Freesurfer 5.0 installed). I want to calculate the volume of a VOI that is not calculated from recon all. I ll decribe you the steps that were followed. Using tkmedit and tkmedit tools i created ROIs in many slices. Every ROI i saved it as label, then i merge all the labels using the mri_mergelabels. I am trying create a volume from this final label using mri_label2vol, using as label the new final label, as template volume the origin volume (orig.mgz) but i don't have the register.dat file. How i can create it? The above way is the appropriate way to calculate a VOI? Thank you in advance! ___ 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] creating a skull
did you try using freeview? For example: freeview -v brain.mgz On Fri, 31 Aug 2012, Borzello, Mia wrote: Hi, I make it an mgz. When trying to load (tried using a load and read command) to make sure it looks okay, but it's not working. How can I view this mgz file or ascertain that it has an error? Thanks, m From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu] Sent: Friday, August 31, 2012 10:29 AM To: Borzello, Mia Cc: freesurfer Subject: Re: [Freesurfer] creating a skull Hi, You need to add an extension onto the file name, something like brain.mgz or brain.nii. The extension will tell it what format to save the output in. -Louis On Fri, 31 Aug 2012, Borzello, Mia wrote: Hi freesurfer family, I am trying to create the inner skull boundary and ran: mri_watershed -atlas - surf -useSRAS mri.nii brain However, after it finished running it said it was saving brain, but brain was an unknown file type. Am i supposed to specify that somewhere? Thanks in advance, m ___ 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 ___ 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] creating a skull
Hi Mia what platform are you running on? Bruce On Fri, 31 Aug 2012, Borzello, Mia wrote: I've been referred to the following link on the freesurfer site to handle this, but is this still current (i.e. is linux still needed to do this?): http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004679.html thanks, m From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu] Sent: Friday, August 31, 2012 10:29 AM To: Borzello, Mia Cc: freesurfer Subject: Re: [Freesurfer] creating a skull Hi, You need to add an extension onto the file name, something like brain.mgz or brain.nii. The extension will tell it what format to save the output in. -Louis On Fri, 31 Aug 2012, Borzello, Mia wrote: Hi freesurfer family, I am trying to create the inner skull boundary and ran: mri_watershed -atlas - surf -useSRAS mri.nii brain However, after it finished running it said it was saving brain, but brain was an unknown file type. Am i supposed to specify that somewhere? Thanks in advance, m ___ 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 ___ 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] FDR Correction of NHP Surface Data
Hi Bruce, Will do. Thanks again. -Clark On Sep 3, 2012, at 2:33 PM, Bruce Fischl wrote: Hi Clark sorry, the end of the summer has been a period when things slip through the cracks. I think what you want is possible without a talairach or aseg, but it will need to wait for Doug to get back. Can you repost at the end of next week? Bruce On Thu, 30 Aug 2012, Clark Fisher wrote: Thanks Michael, I'll look into Nipy's FDR tools. I actually started this thread asking for help getting mri_surfcluster running for my situation (I have no talraich .xfm and no segmentation for my monkeys). The silence on that topic suggest that it might not be possible, or it's at least not known to possible. Thanks again everyone. -Clark On Aug 29, 2012, at 6:55 PM, Michael Waskom wrote: Hi Clark, If you're loading the data into Python anyway to use with PySurfer, Nipy seems to have some utilities to do an FDR correction (docs/source). I've never used these, but they look pretty straightforward. Also it looks like FDR is built into mri_surfcluster. Best, Michael On Wed, Aug 29, 2012 at 2:08 PM, Clark Fisher cfis...@mail.rockefeller.edu wrote: Hi Sebastian, I think you are right, both about tksurfer thresholding and the correct interpretation of FDR. As you point out though, there is some value in having maps that show how relatively well different points on the surface fit your model. At the very least, is there any way to automate the retrieving of the threshold that tksurfer provides? I'd still also be interested in some adjustment to the whole map, if there's a way to do that as well. I could probably find a way to do this in Matlab, but I trust the bug-squishing abilities of the freesurfer community more than I trust my own. -Clark On Aug 28, 2012, at 2:34 PM, Sebastian Moeller wrote: Hi Clark, On Aug 28, 2012, at 11:15 AM, Clark Fisher wrote: Hi Bruce, Thanks. I actually have used this function of tksurfer, but am looking for a way to save the corrected maps, so that they could be manipulated by other tools (for instance, viewed by PySurfer). Does it really correct the map? I thought all it does is figure out the corrected threshold. By the way, if I understand correctly, FDR maps should be considered to be binary, that is you really do not know which voxels might be false positives, so you should not interpret all voxels to be equally significant. Having said that, almost everybody I know still looks at the p-value spatial distribution when looking at those FDR thresholded maps? (then again, I do not know any statistician...) best Sebastian I recognize that this may not be an officially supported functionality, but is there some way to save the adjusted overlays from tksurfer, or create them in some other way? Best, Clark On Aug 28, 2012, at 1:58 PM, Bruce Fischl wrote: Hi Clark you shouldn't need either. Load your overlays then click the button to compute the FDR threshold in the tksurfer configure overlay interface. cheers Bruce On Tue, 28 Aug 2012, Clark Fisher wrote: Ok, maybe I'm making this question too intricate. Here's the short version: How can I FDR correct painted surface significance maps when I have no talraich .xfm file and no cortical segmentation? Thanks again, Clark Hi Freesurfers, I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: 1) I don't have any .xfm files for my monkeys, as I'm working in native space, and 2) Without segmentation, I don't have a good mask to use for the cortex only. My first attempts at work-arounds would be: 1)Try to create an identity .xfm file 2)Use the cortical ribbons from mris_volmask as a cortex mask Should these work? If so, how should I make an identity .xfm file? If not, is there another way to FDR correct my surface data? Thanks, Clark ___ 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,
