Re: [Freesurfer] Trac-all error
Thank you so much, Zeke! That helped a lot. Best, Emad On Mar 10, 2015, at 11:43 PM, zkauf...@nmr.mgh.harvard.edu wrote: Hello Emad, The download page states that OSX versions of freesurfer require the user to download and install XQuartz onto their machine. I have updated the download page so it is a little more clear. https://surfer.nmr.mgh.harvard.edu/fswiki/Download https://surfer.nmr.mgh.harvard.edu/fswiki/Download Also, the dev version of freesurfer is in a high degree of flux right now. We are undergoing compiler upgrades and other various changes to the build. This means I would expect the nightly builds to be unstable for the next couple days. But installing XQuartz should resolve the issue you experienced below. -Zeke Hello Anastasia, Iâm using the nightly-built version for Mac OS Lion; I double checked it by the command freesurfer -ver and got this response: You are running this version of FreeSurfer: freesurfer-Darwin-lion-dev-20150227 Iâm using this version on Mac OS X Yosemite. I tried to re-download a nightly built version, but it didnât let me (presumably because itâs workshop time). Please let me know how I should proceed. Yours, Emad On Mar 6, 2015, at 7:11 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.harvard.edu wrote: Hi Emad - The error is: dyld: Library not loaded: /usr/X11/lib/libGLU.1.dylib Does the freesurfer build that you're using match the computer that you're running it on? a.y On Wed, 4 Mar 2015, Emad Ahmadi wrote: Hello Freesurfers! Iâm trying to use tracheal -prep, and Iâm getting an error. Would you please help me with figuring out where the problem is? The log file is attached. Thank you very much, Emad Emad Ahmadi, MD --- Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] segmentation
Dear Freesurfer users, Does anybody knows if the steps after the segmentation have some impact in subcortical structures volume? If it does, how can I have this measurements back even if I had already run recon-all? best, Maurício Anés ___ 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] Thin Surface
Hi, Bruce. I tried several thresholds in some subjects and it seems to work reallh well. Thanks for the help! However, I would like to ask whether I should determine the expert values based on the raw image (001.mgz) or the normalized image (T1.mgz)? I am asking this because I believe the normalization can change the intensity values a lot. Thanks again, Pedro. On Feb 18, 2015, at 19:58, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: can you check mri_segmet and mris_make_surfaces and see if the auto-detected intensity parameters are reasonable? Things like max gray at csf border and such. If not, you can set them explicitly using the expert opts - this usually works Bruce On Wed, 18 Feb 2015, Pedro Rosa - Gmail wrote: Hi, I am resending it once I could not find it in the archives. Thanks, Pedro. Dear Freesurfers, I am working on a 1.5T MPRAGE sample of first-episode psychosis and controls, and have found that some subjects end up having thin cortical surfaces with frequent unsegmented deep sulci. I think this was worse with FreeSurfer 5.3 than with FreeSurfer 5.1. I attached some screen shots of aparc+aseg labeling T1.mgz from a few of these subjects. This seems to be a widespread cortical issue, although it was heterogeneous across subjects (some of them seemed to have the “caudal half of both hemispheres adequately segmented), and trying to simply rerun those subjects was not very helpful. Should I manually work on them, rerun recon-all with distinct parameters, or just discard them? Regards, Pedro Rosa. ___ 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] [FreeSurfer] Visualize Compute Overlaps between two significant surface maps
Thank you Douglas I will try this. Matthieu Vanhoutte, MSc Research Engineer - Neuroradiology Department Regional University Hospital, Lille, France Le 16 mars 2015 19:13, Douglas N Greve gr...@nmr.mgh.harvard.edu a écrit : For visualizing the overlap, I would probably create a segmentation in which each vertex is either 1 (present in thickness), 2 (present in CBF), or 3 present in both. You can do this in matlab or with a combination of mri_binarize and fscalc. You can then create an annotation from the seg with mris_seg2annot. I would compute a dice coefficent of the overlap in matlab, something like dice = n12/((n1+n2)/2) where n1 is the number of vetices in thick, n2 for cbf, and n12 is the number that overlap doug On 03/16/2015 12:09 PM, Matthieu Vanhoutte wrote: Dear FreeSurer's experts, I used group analysis based on GLM to compute significative surface maps of different characteristics : thickness, CBF,... Now I've got these maps I would like to visualize overlaps between two different maps and compute the overlap ratio. How could I succeed these two steps ? Best regards, - Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France ___ 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 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] Dealing with hyper-intensities
Hi Cassie those are the result of low bandwidth and susceptibility artifacts. There's not much that can be done about them post-hoc - the images don't contain enough information to reconstruct accurate models in those regions. In general we recommend higher bandwidth sequences for this reason, ideall multi-echo mprage sorry Bruce On Mon, 16 Mar 2015, Cassandra Wannan wrote: Hi guys, I am quite new to Freesurfer and am having some issues with hyper-intensities in the set of scans I am working on. The spots are appearing mainly in GM in the inferior temporal lobes and the orbitofrontal cortex, and seem to be in all of the scans I have looked at so far from my data set (these are old 1.5T scans from the late 90's). I don't know if there is anything to be done about the issue, but any advice would be greatly appreciated, particularly as both of these regions are ROIs for my study. In some areas, it doesn't look as though the hyper-intensities have affected the wm or pail boundaries, but in others they clearly have. Cheers, Cassie ___ 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] mri_glmfit error FSGD file exceeds the maximum allowed 2000
FreeSurfer List, I am attempting to run an analyses on 2051 participants. However, when I reach the mri_glmfit stage I receive the following error. ERROR: gdfReadV1: the number of inputs in FSGD file exceeds the maximum allowed 2000 Is there a work around for this? Thank you in advance for any help you can offer, Avram Avram Holmes PhD Assistant Professor Department of Psychology, Yale University Email: avram.hol...@yale.edu Office: 203-436-9240 Web: holmeslab.commons.yale.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.
[Freesurfer] [FreeSurfer] Visualize Compute Overlaps between two significant surface maps
Dear FreeSurer's experts, I used group analysis based on GLM to compute significative surface maps of different characteristics : thickness, CBF,... Now I've got these maps I would like to visualize overlaps between two different maps and compute the overlap ratio. How could I succeed these two steps ? Best regards, - Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France ___ 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] mri_glmfit with fractional values in contrast file .mtx
Dear experts, Could you indicate me how to specify a contrast vector with fractional values ? I tried the below formats without success in the .mtx file: [0 0 0 0 0 0 1 1 1 -1 -1 -1]/3 |0 0 0 0 0 0 1 1 1 -1 -1 -1|/3 0 0 0 0 0 0 1/3 1/3 1/3 -1/3 -1/3 -1/3 Thank in advance for helping ! Best regards, - Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France ___ 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] MNIX/Y/Z coordinates in mri_glmfit-sim .summary file
They are MNI305 coordinates. When we mention Talairach coordinates, it refers to mni305 coordinates that have been transformed according to some work done by Matthew Brett. It used to be documented here http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html, but it is not in that location anymore doug On 03/15/2015 04:10 PM, Nicola Toschi wrote: Hi list, I noticed that, while the wiki refers to Talairach coordinates named TalX/Y/Z (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary), the header in my .summary files reads something like: # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWP CWPLowCWPHi NVtxs Annot could someone confirm what atlas space the MINX/MINY/MNIZ coordinates are in? Is it Talairach, MNI152 or something else? Thanks in advance, Nicola ___ 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.
Re: [Freesurfer] [FreeSurfer] mri_glmfit with fractional values in contrast file .mtx
you'll need to use .33 On 03/16/2015 11:09 AM, Matthieu Vanhoutte wrote: Dear experts, Could you indicate me how to specify a contrast vector with fractional values ? I tried the below formats without success in the .mtx file: [0 0 0 0 0 0 1 1 1 -1 -1 -1]/3 |0 0 0 0 0 0 1 1 1 -1 -1 -1|/3 0 0 0 0 0 0 1/3 1/3 1/3 -1/3 -1/3 -1/3 Thank in advance for helping ! Best regards, - Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France ___ 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.
Re: [Freesurfer] mri_glmfit error FSGD file exceeds the maximum allowed 2000
This is hard coded unfortunately. I've bumped it up to 20k in the most recent version. I've put a linux version here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit On 03/16/2015 06:38 AM, Avram Holmes wrote: FreeSurfer List, I am attempting to run an analyses on 2051 participants. However, when I reach the mri_glmfit stage I receive the following error. ERROR: gdfReadV1: the number of inputs in FSGD file exceeds the maximum allowed 2000 Is there a work around for this? Thank you in advance for any help you can offer, Avram Avram Holmes PhD Assistant Professor Department of Psychology, Yale University Email: avram.hol...@yale.edu mailto:avram.hol...@yale.edu Office: 203-436-9240 Web: holmeslab.commons.yale.edu http://holmeslab.commons.yale.edu ___ 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.
Re: [Freesurfer] [FreeSurfer] Visualize Compute Overlaps between two significant surface maps
For visualizing the overlap, I would probably create a segmentation in which each vertex is either 1 (present in thickness), 2 (present in CBF), or 3 present in both. You can do this in matlab or with a combination of mri_binarize and fscalc. You can then create an annotation from the seg with mris_seg2annot. I would compute a dice coefficent of the overlap in matlab, something like dice = n12/((n1+n2)/2) where n1 is the number of vetices in thick, n2 for cbf, and n12 is the number that overlap doug On 03/16/2015 12:09 PM, Matthieu Vanhoutte wrote: Dear FreeSurer's experts, I used group analysis based on GLM to compute significative surface maps of different characteristics : thickness, CBF,... Now I've got these maps I would like to visualize overlaps between two different maps and compute the overlap ratio. How could I succeed these two steps ? Best regards, - Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France ___ 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] Reading retinotopy output (eccentricity/polar) into Matlab in correct space for SPM
Hi all, I’m new to both freesurfer and fMRI, and after reading some related posts on the forum I still can't complete this task so would appreciate any help or suggestions. I’m trying to import the eccentricity and polar maps from a freesurfer retinotopy analysis into matlab. My goal is to have a matlab matrix which specifies the eccentricity and polar angle (or separate matrices for polar and ecc.) of every voxel in V1, which I can then link to my MVPA analysis (done with Matlab and SPM). So I also need to link the eccentricity/polar coordinates to the coordinates of the voxels as they are organised in SPM (as a 3D matrix with the location of each voxel in the matrix corresponding to its location in the structural MRI volume). So far, I’ve located the freesurfer matlab toolbox and used MRIread to read in the eccentricity and polar .nii.gz files. But because of my limited freesurfer knowledge, I'm unsure of the next step. Which of the freesurfer output files/variables do I actually want? I see there are real and imaginary components separately for the left and right hemispheres, for both eccentricity and polar. How can I combine these so that I end up with a 3D matrix containing the eccentricity (or polar) value for each voxel, with the location of the voxels in the 3D matrix corresponding to its location in the MRI volume (as in SPM)? thanks in advance, any suggestions are very welcome Susan ___ 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] mri_glmfit with fractional values in contrast file .mtx
Thank you Douglas. Matthieu Vanhoutte, MSc Research Engineer - Neuroradiology Department Regional University Hospital, Lille, France Le 16 mars 2015 18:17, Douglas N Greve gr...@nmr.mgh.harvard.edu a écrit : you'll need to use .33 On 03/16/2015 11:09 AM, Matthieu Vanhoutte wrote: Dear experts, Could you indicate me how to specify a contrast vector with fractional values ? I tried the below formats without success in the .mtx file: [0 0 0 0 0 0 1 1 1 -1 -1 -1]/3 |0 0 0 0 0 0 1 1 1 -1 -1 -1|/3 0 0 0 0 0 0 1/3 1/3 1/3 -1/3 -1/3 -1/3 Thank in advance for helping ! Best regards, - Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France ___ 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 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] Drawing ROIs using coordinates in another space?
Hi all, I'm working with BrainVoyager and Freesurfer. I have some Talairach coordinates from BV for a functional ROI, and I'm trying to see if I can use these coordinates in Freesurfer to draw the same ROI on the structural slices. Is this possible? Alternatively, is it possible to draw a sphere ROI in Freesurfer that will be applied to all my subjects for group-level comparisons? Any help would be greatly appreciated! Best, Natalie -- Natalie V. Garcia Graduate Fellow, Cognitive Neuroscience Department of Psychology The Pennsylvania State University 423 Moore Building University Park, PA 16802 nvg...@psu.edu http://sites.psu.edu/scherflab/ ___ 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.
