Re: [Freesurfer] Label or Overlay of Surface files
And are they treated as label files (e.g. lh.aparc.annot ) in the label directory? And how they can be added to the tksurfer snapshot procedure? On Thu, Aug 6, 2015 at 4:04 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: no, the scalar overlays are stored separately (e.g. lh.curv, lh.sulc, etc...) On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, Is scalar overlay information embedded into surface file itself? When I open them in freeview they are loaded with color overlays (sulcus/gyrus), but when I load same models into 3D slicer or take a snapshot in tksurfer, they are plain gray. Thanks, Saeed ___ 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] Label or Overlay of Surface files
I used it as this: tksurfer subject hemisphere surface -snap file name -overlay file name And it adds a* gray scale* version of sulcus map to the plain gray, How can I activate colors? Thanks, Saeed On Thu, Aug 6, 2015 at 4:20 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: load them as curvature files cheers Bruce On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: And are they treated as label files (e.g. lh.aparc.annot ) in the label directory? And how they can be added to the tksurfer snapshot procedure? On Thu, Aug 6, 2015 at 4:04 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: no, the scalar overlays are stored separately (e.g. lh.curv, lh.sulc, etc...) On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, Is scalar overlay information embedded into surface file itself? When I open them in freeview they are loaded with color overlays (sulcus/gyrus), but when I load same models into 3D slicer or take a snapshot in tksurfer, they are plain gray. Thanks, Saeed ___ 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 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] (no subject)
Hello, Thank you for the report. Can you please provide a simplified context of how this came about... meaning, does the crash ONLY occur when you alter the contents of a file? Does the crash ever occur during a normal recon? Many files in freesurfer are read on a bite-wise basis and if the contents are changed manually than the slightest offset can cause anything from invalid values read into the data structure, to possible seg faults, and/or program crashing. I could possibly investigate, but if you wish to have unstripped binaries I can provide that as well. If you intend to pursue this further please contact my direct email address to prevent spamming the list on this detailed matter. Thanks. -Zeke On 08/06/2015 01:42 AM, Lionel zorzevic wrote: Hi, The recon pipeline outputed an apparently correct file, which happen to confuse freesurfer reading functions. I attached a slightly-altered file named lh.data_crash which have the same problem. The other file named lh.data_nocrash seems to be parsed fine, despite differing by only 1 float-value somewhere in the middle of the data section. Original file was lh.area The mri_info command outputs some meaningless values; and the mris_calc command bails out. $ mri_info lh.data_crash WARNING: # of slices=-45 in header - assuming 124... Volume information for lh.data_crash type: unknown dimensions: 3391 x 2677 x 124 voxel sizes: -0., -0., -0. type: SHORT (4) fov: 0.246 dof: 0 xstart: 548.5, xend: 5149214485235471024091229374082187264.0 ystart: -0.0, yend: -0.0 zstart: -1008284058362807724504196555655348224.0, zend: 0.0 ... $ mri_info lh.data_nocrash Volume information for lh.data_nocrash type: curv dimensions: 124254 x 1 x 1 voxel sizes: 1., 1., 1. type: FLOAT (3) fov: 124254.000 dof: 0 xstart: -62127.0, xend: 62127.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.0 ... The difference between the two files are a single value change (4 bytes) at offset 1095 (15+4*1095'th byte), although other alteration are possible which avoid the crash too. This happens on Freesurfer version 5.3.0, and also 5.1.0, and 6-beta, on all arch i could test, which are RedHat 6.6 (64bits), Ubuntu 10.x (32bits), and MacOSX 10.8 (64bits) Note: to preserve privacy, the original map values have been replaced by a dummy 42.0 for most of the file, since i believe actual data is irrelevant here. I couldn't track the problem further, as i only have (stripped) binaries here. ___ 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] Label or Overlay of Surface files
no, the scalar overlays are stored separately (e.g. lh.curv, lh.sulc, etc...) On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, Is scalar overlay information embedded into surface file itself? When I open them in freeview they are loaded with color overlays (sulcus/gyrus), but when I load same models into 3D slicer or take a snapshot in tksurfer, they are plain gray. Thanks, Saeed ___ 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] FSFAST
Hi all,If I understand correctly, preproc-sess command takes mid point of EPI image as reference and make template and calculate motion parameters. I could not figure if I could use different image as reference, is it possible? Cheers, Sabin Khadka___ 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] Label or Overlay of Surface files
load them as curvature files cheers Bruce On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: And are they treated as label files (e.g. lh.aparc.annot ) in the label directory? And how they can be added to the tksurfer snapshot procedure? On Thu, Aug 6, 2015 at 4:04 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: no, the scalar overlays are stored separately (e.g. lh.curv, lh.sulc, etc...) On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, Is scalar overlay information embedded into surface file itself? When I open them in freeview they are loaded with color overlays (sulcus/gyrus), but when I load same models into 3D slicer or take a snapshot in tksurfer, they are plain gray. Thanks, Saeed ___ 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] mkanalysis-sess, timewindow
The second number in the psdwin parameter is set as 40 in the flac_ev_parse.m for 'spmhrf', 'gamma', 'fslgamma'. It seems that timewindow has no effect on hrf? why is psdwin 40? Thanks, Xiaomin From: yu...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Thu, 6 Aug 2015 15:17:04 -0400 Subject: Re: [Freesurfer] mkanalysis-sess, timewindow if it is useful, i can upload the Xtmp.mat file. thanks, Xiaomin Date: Thu, 6 Aug 2015 10:36:50 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mkanalysis-sess, timewindow it would be helpful to have your mkanalysis-sess command On 08/05/2015 04:17 PM, Xiaomin Yue wrote: Hi, I set timewindow to 10 in the mkanalysis-sess. When I loaded Xtmp.mat in to maltlab, then plot(flac.ev(2).Xirf), the size of the flac.ev(2).Xirf is 20 points, which is corrected because of psdwin is [0 40 2]. Should the psdwin be [0 10 2]? No matter what value I put in to timewindow, the psdwin is alway [0 40 2]. Is it correct? If so, what aspect of design matrix does the timewidow have effect on? thanks very much for your help. Xiaomin ___ 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 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] Label or Overlay of Surface files
Hi Saeed, You can run either of the following commands to overlay the ?h.sulc or ?h.curv file: tksurfer subject hemisphere surface -snap file name -sulc tksurfer subject hemisphere surface -snap file name -curv Best, Lee On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: I used it as this:tksurfer subject hemisphere surface -snap file name -overlay file name And it adds a gray scale version of sulcus map to the plain gray, How can I activate colors? Thanks, Saeed On Thu, Aug 6, 2015 at 4:20 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: load them as curvature files cheers Bruce On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: And are they treated as label files (e.g. lh.aparc.annot ) in the label directory? And how they can be added to the tksurfer snapshot procedure? On Thu, Aug 6, 2015 at 4:04 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: no, the scalar overlays are stored separately (e.g. lh.curv, lh.sulc, etc...) On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, Is scalar overlay information embedded into surface file itself? When I open them in freeview they are loaded with color overlays (sulcus/gyrus), but when I load same models into 3D slicer or take a snapshot in tksurfer, they are plain gray. Thanks, Saeed ___ 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 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] Weird Freesurfer results
Thanks, Dr. Fischl. Original image and recon: + brainmask.mgz (1.27 MiB) http://gate.nmr.mgh.harvard.edu/filedrop2/?p=agy57k1qjyh + lh.pial (4.33 MiB) http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1k79w4nsitw + lh.white (4.33 MiB) http://gate.nmr.mgh.harvard.edu/filedrop2/?p=90gq0da66ar + rh.pial (4.29 MiB) http://gate.nmr.mgh.harvard.edu/filedrop2/?p=afmeea5gzmq + rh.white (4.29 MiB) http://gate.nmr.mgh.harvard.edu/filedrop2/?p=96jsu9l1wkx Synthethic image and recon: + brainmask.mgz (1.27 MiB) http://gate.nmr.mgh.harvard.edu/filedrop2/?p=96pjr5j7y9g + lh.pial (4.33 MiB) http://gate.nmr.mgh.harvard.edu/filedrop2/?p=91u587oukvs + lh.white (4.33 MiB) http://gate.nmr.mgh.harvard.edu/filedrop2/?p=7stlc9abt4k + rh.pial (4.32 MiB) http://gate.nmr.mgh.harvard.edu/filedrop2/?p=66g81vebmo3 + rh.white (4.32 MiB) http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1kc9lmgx2dx Area where we expect to see a change: 107 79 176 Areas where we found unexpected changes: 82 131 102 153 84 106 145 137 149 84 114 168 107 92 170 -Brent On Thu, Aug 6, 2015 at 12:35 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Brent if you upload the subjects and point us at the specific locations you expect to see effects and the ones you don't we will take a look cheers Bruce On Thu, 6 Aug 2015, Brent Womble wrote: So I'm making changes to the intensity values in a specific area (a sphere or several slices, depending on the technique). I'm getting recons that are inconsistent in areas where the 2 images are exactly the same (far away from the changes I made). I can't figure out why. Where should I go from here? -Brent On Tue, Aug 4, 2015 at 2:08 PM, Brent Womble brentwom...@gmail.com wrote: Yes, I completely agree. In this project, I'm simulating 3 possible changes: an expanded gyrus, a folded gyrus, and a denser gyrus (see poster here). The poster goes into more detail on the rationale for these 3 possible changes. I'm using these relatively focal changes because I'm modeling use-dependent structural neuroplasticity, not atrophy. I'm using a different method for the expanded/folded gyrus than the denser gyrus (see poster). The changes I make in the expanded/folded gyrus propagate through the entire slice. Here is a difference image from the center of the deformation: [IMAGE] Here is a difference image from a slice at the far end of the deformation (where the in-plane deformation is smallest): [IMAGE] I'm getting noisy results in all 3 datasets (in areas far away from the actual changes). I sent around the denser gyrus dataset first because it was simplest. On Tue, Aug 4, 2015 at 12:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: What you really want to simulate is an underlying geometric deformation (like atrophy) that gets propagated through an image formation model to create an atrophic image. I don't think multiplying the image intensities is a good model for what you want. Atrophy doesn't look like a uniform darkening of the gray matter. On Tue, 4 Aug 2015, Brent Womble wrote: Yes, I'm multiplying the image intensities by a scaling factor. Sorry if that wasn't clear. -Brent On Aug 4, 2015 12:09, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Brent a quick look and it seems that your answer is yes? You are multiplying the image intensities by some scale factor? Bruce On Tue, 4 Aug 2015, Brent Womble wrote: Yes. Here is the MATLAB script: for i = [1:20] %Load the original image and gray matter mask raw=load_nii([pwd,'/', num2str(i), '/pre.nii']) a=single(squeeze(raw.img)); c1_raw=load_nii([pwd,'/', num2str(i), '/c1pre.nii']); c1=squeeze(c1_raw.img); %Mask is gray around edges. Threshold to make it binary c1(c10.1)=1; %Convert mask to logical c1=logical(c1); %%Generate a 3D gaussian kernel %Specify the origin, size, and intensity of the kernel k_origin=origins(i,:); %origins is an i by 3 vector to store all coordinates k_size=20;
Re: [Freesurfer] how to obtain sulcal depth in a given region for a specific subject
Thanks so much for your help!! - Daniel On 8/6/15, 3:06 PM, freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu wrote: ignore grayvol, the other two will be the mean and standard deviation of the sulc cheers Bruce On Thu, 6 Aug 2015, Yang, Daniel wrote: Hi Bruce, Thanks so much! From the output of mris_anatomical_stats, I can see that it affects the following three variables: GrayVol ThickAvg ThickStd When sulc is used instead of thickness, do you know what the meaning of these three variables is changed to? Many thanks, Daniel On 8/6/15, 1:35 PM, freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu wrote: sure, you can use mris_anatomical_stats with the label (-l) and specify sulc instead of thickness on the command line Bruce On Thu, 6 Aug 2015, Yang, Daniel wrote: Dear FreeSurfer Experts, Is there a way to obtain sulcal depth in a given region (label) for a particular subject? Many thanks! Daniel ___ 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_com pl iancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58r xz UZGOKpGXPDgqUHYm=xyE0RdUufB5jqZcisLNchEsdjJ5ZrxPKb_nS1NUHf6As=f9y2eo81 NI x6DddRv7BfTBuLWMoaGFQAWMNMlqXCD7se= . 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 ___ 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl iancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxz UZGOKpGXPDgqUHYm=MGg2posyaqsYcBQNPMfU8se8ukFgyZ7f-Oe0LQdl9aAs=yl0bAVXLDZ -FAqiDaW-T036lJiy1KcmDmqmve98TXQce= . 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] Label or Overlay of Surface files
Hello, Is scalar overlay information embedded into surface file itself? When I open them in freeview they are loaded with color overlays (sulcus/gyrus), but when I load same models into 3D slicer or take a snapshot in tksurfer, they are plain gray. Thanks, Saeed ___ 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] Fwd: Inflated and Spherical Morphing --- Step by step surfaces
Ok, but how about the mophing process? Isn't inflated brain transformed to the sphere directly? Is there a middle step that is hidden (e.g. inflatted to the brain flat maps and spreading these maps over the sphere)? I want to generate a contineous transformation video from WM to inflated and inflated to a sphere. On Aug 6, 2015 7:45 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: yes, because it is unfolding on the sphere to recover metric properties. -w 1 gives you every iteration. You will need to show curvature or you won't see anything On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, What are your suggested values for w and n in mris_sphere? I set w to 5 and all of the iterations are spheres! Thanks, Saeed On Wed, Aug 5, 2015 at 1:06 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Saeed if you specify -w n to mris_inflate or mris_sphere it will save snapshots of the process every nth iteration cheers Bruce On Wed, 5 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, Since surface deformation from WM to inflated surface is a gradual process, I assume that interim surfaces can also be saved and visualized, as I have seen in the ppt of Analyzing the Individual Subject tutorial session (slide #32). I am curious to know which command and options can generate that type of gradual deformations from pial surface to spherical surface, so that viewer can visually track region or points of interest? Best, Saeed ___ 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 ___ 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] Fwd: Inflated and Spherical Morphing --- Step by step surfaces
Hello, What are your suggested values for *w* and *n* in *mris_sphere*? I set *w* to 5 and all of the iterations are spheres! Thanks, Saeed On Wed, Aug 5, 2015 at 1:06 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Saeed if you specify -w n to mris_inflate or mris_sphere it will save snapshots of the process every nth iteration cheers Bruce On Wed, 5 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, Since surface deformation from WM to inflated surface is a gradual process, I assume that interim surfaces can also be saved and visualized, as I have seen in the ppt of Analyzing the Individual Subject tutorial session (slide #32). I am curious to know which command and options can generate that type of gradual deformations from pial surface to spherical surface, so that viewer can visually track region or points of interest? Best, Saeed ___ 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] Announcing PySurfer version 0.6
Hello everyone, We are pleased to announce the 0.6 release of PySurfer http://pysurfer.github.io/, a Python library for visualizing MRI and MEG data. Changes in this version include: - Simplified the selection of parameters that customize the visualization - Enhanced plotting of Freesurfer morphometry overlays (thickness, curvature, etc.) - Enhanced plotting of statistical overlays using contour maps - Improved support for scripted animation of the brain visualization See the release notes https://github.com/nipy/PySurfer/releases/tag/0.6 for more details about these changes. For information on installation, documentation, and the example gallery, you can visit our website (http://pysurfer.github.com/). We hope you will find it useful in your research! Michael Waskom, Eric Larson, Christian Brodbeck, and the rest of the Nipy team ___ 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] Fwd: Inflated and Spherical Morphing --- Step by step surfaces
yes, because it is unfolding on the sphere to recover metric properties. -w 1 gives you every iteration. You will need to show curvature or you won't see anything On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, What are your suggested values for w and n in mris_sphere? I set w to 5 and all of the iterations are spheres! Thanks, Saeed On Wed, Aug 5, 2015 at 1:06 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Saeed if you specify -w n to mris_inflate or mris_sphere it will save snapshots of the process every nth iteration cheers Bruce On Wed, 5 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, Since surface deformation from WM to inflated surface is a gradual process, I assume that interim surfaces can also be saved and visualized, as I have seen in the ppt of Analyzing the Individual Subject tutorial session (slide #32). I am curious to know which command and options can generate that type of gradual deformations from pial surface to spherical surface, so that viewer can visually track region or points of interest? Best, Saeed ___ 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] Fornix Segmentation
Hi Maryam try specifying -f on the mri_cc command line (as the first option) cheers Bruce On Thu, 6 Aug 2015, Syeda Maryam wrote: Hi everyone, So I've been going through the list trying to see if someone has encountered the same problem as me with regards to segmentation of the fornix but have not found a solution as yet. I'm a grad student and still relatively new to freesurfer. My research group is using freesurfer to segment and visualize white matter tracts in data obtained from the ADNI database. We are primarily working with the subcortical segmentation in the aseg volume. My current issue is that I am unable to find the labels for the fornix in the aseg volume; they seem to only be located in the wm volume generated by freesurfer. When I try to run mri_cc on my aseg, the corpus callosum and fornix segmentation are output together and I'm unable to analyze them separately. I'd really like all the labels I require to be contained in a single volume rather than multiple ones as that will make my job a lot easier. Is there something I'm missing? Is there a way of extracting the fornix and corpus callosum, and indeed, all white matter tracts from the same volume? Any help will be highly appreciated! Thanks in advance, Maryam ___ 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 to obtain sulcal depth in a given region for a specific subject
sure, you can use mris_anatomical_stats with the label (-l) and specify sulc instead of thickness on the command line Bruce On Thu, 6 Aug 2015, Yang, Daniel wrote: Dear FreeSurfer Experts, Is there a way to obtain sulcal depth in a given region (label) for a particular subject? Many thanks! Daniel ___ 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] Fornix Segmentation
Yes, I was able to locate that file. Thank again! Don't know how I managed to miss it the first time! Regards,Maryam On Thursday, August 6, 2015 1:35 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: does it not say writing fornix to mri/fornix.mgz and write out a separate file? The other thing you could consider is using tracula for this, which I think will work even in the absence of diffusion data. cheers Bruce On Thu, 6 Aug 2015, Syeda Maryam wrote: Hi Bruce, Thanks so much for getting back to me on this! Yes, I have tried mri_cc with -f and I am able to view part of the fornix along with the corpus callosum when I call up the appropriate labels. However, I don't seem to be able to visualize the two structures separately. Is it possible to separate the two? Thanks in advance! Regards, Maryam On Thursday, August 6, 2015 1:22 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Maryam try specifying -f on the mri_cc command line (as the first option) cheers Bruce On Thu, 6 Aug 2015, Syeda Maryam wrote: Hi everyone, So I've been going through the list trying to see if someone has encountered the same problem as me with regards to segmentation of the fornix but have not found a solution as yet. I'm a grad student and still relatively new to freesurfer. My research group is using freesurfer to segment and visualize white matter tracts in data obtained from the ADNI database. We are primarily working with the subcortical segmentation in the aseg volume. My current issue is that I am unable to find the labels for the fornix in the aseg volume; they seem to only be located in the wm volume generated by freesurfer. When I try to run mri_cc on my aseg, the corpus callosum and fornix segmentation are output together and I'm unable to analyze them separately. I'd really like all the labels I require to be contained in a single volume rather than multiple ones as that will make my job a lot easier. Is there something I'm missing? Is there a way of extracting the fornix and corpus callosum, and indeed, all white matter tracts from the same volume? Any help will be highly appreciated! Thanks in advance, Maryam ___ 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 ___ 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] Fornix Segmentation
Hi Bruce, Thanks so much for getting back to me on this! Yes, I have tried mri_cc with -f and I am able to view part of the fornix along with the corpus callosum when I call up the appropriate labels. However, I don't seem to be able to visualize the two structures separately. Is it possible to separate the two? Thanks in advance! Regards,Maryam On Thursday, August 6, 2015 1:22 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Maryam try specifying -f on the mri_cc command line (as the first option) cheers Bruce On Thu, 6 Aug 2015, Syeda Maryam wrote: Hi everyone, So I've been going through the list trying to see if someone has encountered the same problem as me with regards to segmentation of the fornix but have not found a solution as yet. I'm a grad student and still relatively new to freesurfer. My research group is using freesurfer to segment and visualize white matter tracts in data obtained from the ADNI database. We are primarily working with the subcortical segmentation in the aseg volume. My current issue is that I am unable to find the labels for the fornix in the aseg volume; they seem to only be located in the wm volume generated by freesurfer. When I try to run mri_cc on my aseg, the corpus callosum and fornix segmentation are output together and I'm unable to analyze them separately. I'd really like all the labels I require to be contained in a single volume rather than multiple ones as that will make my job a lot easier. Is there something I'm missing? Is there a way of extracting the fornix and corpus callosum, and indeed, all white matter tracts from the same volume? Any help will be highly appreciated! Thanks in advance, Maryam ___ 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] Changing Color Labels
Hi freesurfer experts! Sorry if this is a basic question, but I have a manual parcellations for the cortex of the temporal lobe. The problem is that since my voxel size is 0.38, 0.38, 0.38, I converted it to 1 mm voxel size (which I did using mri_convert -c) so that I can compare it to, but the color labels are all mixed up. Is there a way to make all the color labels into one single color label without manual editing each one? I need to be able to use mri_compute_overlap to compare the parcellations, and they won't work unless they are equal voxel size. Thank you and best, Owais ___ 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] mkanalysis-sess, timewindow
if it is useful, i can upload the Xtmp.mat file. thanks, Xiaomin Date: Thu, 6 Aug 2015 10:36:50 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mkanalysis-sess, timewindow it would be helpful to have your mkanalysis-sess command On 08/05/2015 04:17 PM, Xiaomin Yue wrote: Hi, I set timewindow to 10 in the mkanalysis-sess. When I loaded Xtmp.mat in to maltlab, then plot(flac.ev(2).Xirf), the size of the flac.ev(2).Xirf is 20 points, which is corrected because of psdwin is [0 40 2]. Should the psdwin be [0 10 2]? No matter what value I put in to timewindow, the psdwin is alway [0 40 2]. Is it correct? If so, what aspect of design matrix does the timewidow have effect on? thanks very much for your help. Xiaomin ___ 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] how to obtain sulcal depth in a given region for a specific subject
Dear FreeSurfer Experts, Is there a way to obtain sulcal depth in a given region (label) for a particular subject? Many thanks! Daniel ___ 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] wm parcellation freesurfer
That was it! (and yes, we were trying to have freesurfer do an autoparcellation for higher resolution MRI, but the full reconstruction unfortunately keeps failing on processes like skull strip). But for now, we will use the 1 mm reconstruction. Thank you for the help! Owais On Mon, Aug 3, 2015 at 12:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Owais are your voxels really .36mm isotropic? That is extremely high resolution and very very rare (and hard!) if you are getting whole-brain coverage. You can use -cm in recon-all (conform to min) to keep the resolution, but everything will take way longer and use way more memory. I would check to see what the true resolution of your data is first though. cheers Bruce On Mon, 3 Aug 2015, Owais Syed wrote: Thanks for the reply, I think I misspoke though. My original T1 MRI has a voxel size of 0.36, 0.36, 0.36. But when I am looking through the files created via recon -all (specifically wmparc.mgz, although present in other files as well), I noticed that the voxel size is a bit larger (about 1, 1, 1). Is there a way to edit the voxel size to match the MRI during recon -all? Also how would I do that specifically for just creating wmparc.mgz from the original T1 MRI? If it is possible to do so that would be nice, otherwise I will probably try to run the entire recon -all with the new voxel size. Thanks, Owais On Wed, Jul 29, 2015 at 11:25 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Owais do you mean the wmparc.mgz or the aparc+aseg.mgz? You can use mris_divide_parcellation or mris_make_face_parcellation to subdivide or make an isotropic finer scale one if you want. I believe that you can then create a new aparc+aseg from one of those and then the wmparc from that to get a finer one cheers Bruce On Tue, 28 Jul 2015, Owais Syed wrote: Hi, Is it possible to increase the number of parcellations when making the aparc+aseg file? I have a high resolution MRI, and one parcellation will match every three slides, but I want a better match overall. Thanks, Owais ___ 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. -- Owais Syed Chemistry, Psychology Rice University Class of 2016 ___ 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. -- Owais Syed Chemistry, Psychology Rice University Class of 2016 ___ 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 to obtain sulcal depth in a given region for a specific subject
ignore grayvol, the other two will be the mean and standard deviation of the sulc cheers Bruce On Thu, 6 Aug 2015, Yang, Daniel wrote: Hi Bruce, Thanks so much! From the output of mris_anatomical_stats, I can see that it affects the following three variables: GrayVol ThickAvg ThickStd When sulc is used instead of thickness, do you know what the meaning of these three variables is changed to? Many thanks, Daniel On 8/6/15, 1:35 PM, freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu wrote: sure, you can use mris_anatomical_stats with the label (-l) and specify sulc instead of thickness on the command line Bruce On Thu, 6 Aug 2015, Yang, Daniel wrote: Dear FreeSurfer Experts, Is there a way to obtain sulcal depth in a given region (label) for a particular subject? Many thanks! Daniel ___ 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl iancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxz UZGOKpGXPDgqUHYm=xyE0RdUufB5jqZcisLNchEsdjJ5ZrxPKb_nS1NUHf6As=f9y2eo81NI x6DddRv7BfTBuLWMoaGFQAWMNMlqXCD7se= . 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 ___ 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] Changing Color Labels
use nearest neighbor interpolation. Also, probabaly better to use mri_label2vol instead On 08/06/2015 02:17 PM, Owais Syed wrote: Hi freesurfer experts! Sorry if this is a basic question, but I have a manual parcellations for the cortex of the temporal lobe. The problem is that since my voxel size is 0.38, 0.38, 0.38, I converted it to 1 mm voxel size (which I did using mri_convert -c) so that I can compare it to, but the color labels are all mixed up. Is there a way to make all the color labels into one single color label without manual editing each one? I need to be able to use mri_compute_overlap to compare the parcellations, and they won't work unless they are equal voxel size. Thank you and best, Owais ___ 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] how to obtain sulcal depth in a given region for a specific subject
Hi Bruce, Thanks so much! From the output of mris_anatomical_stats, I can see that it affects the following three variables: GrayVol ThickAvg ThickStd When sulc is used instead of thickness, do you know what the meaning of these three variables is changed to? Many thanks, Daniel On 8/6/15, 1:35 PM, freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu wrote: sure, you can use mris_anatomical_stats with the label (-l) and specify sulc instead of thickness on the command line Bruce On Thu, 6 Aug 2015, Yang, Daniel wrote: Dear FreeSurfer Experts, Is there a way to obtain sulcal depth in a given region (label) for a particular subject? Many thanks! Daniel ___ 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl iancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxz UZGOKpGXPDgqUHYm=xyE0RdUufB5jqZcisLNchEsdjJ5ZrxPKb_nS1NUHf6As=f9y2eo81NI x6DddRv7BfTBuLWMoaGFQAWMNMlqXCD7se= . 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] mkanalysis-sess, timewindow
Hi, Doug, Thanks for your response. Here is my command: mkanalysis-sess -fsd bold -paradigm xy_mky_category_eye_weights.par -event-related -refeventdur 1 -timewindow 10 -TER 2 -no-inorm -delay 0 -polyfit 3 -gammafit 0 8 -gammaexp 0.3 -nuisreg mcprextreg 3 -nuisreg eye_movTR_xy 2 -nuisreg fsl_DAVRS 1 -TR 2. -ncondition 940 -funcstem f.mc.perrun.so.nativespace.nii -abcbins 3 -analysis perrun_eye_weights_eyeMovTRxy_tpe_fslmotoutlier -per-run -native -force -tpexclude xy_eye_tpe -runlistfile xyrunlist After running selxavg3-sess, I loaded Xtmp.mat into matlab. The psdwin under flac.ev(2) is [0 40 2]. I also tried to change the timewindow to 20 in the mkanalysis-sess, the psdwin is still [0 40 2]. If I changed the TER to 0.5 , the psdwin is [0 40 0.5] no matter timewindow is 10 or 20. Thanks for looking into this, Xiaomin Date: Thu, 6 Aug 2015 10:36:50 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mkanalysis-sess, timewindow it would be helpful to have your mkanalysis-sess command On 08/05/2015 04:17 PM, Xiaomin Yue wrote: Hi, I set timewindow to 10 in the mkanalysis-sess. When I loaded Xtmp.mat in to maltlab, then plot(flac.ev(2).Xirf), the size of the flac.ev(2).Xirf is 20 points, which is corrected because of psdwin is [0 40 2]. Should the psdwin be [0 10 2]? No matter what value I put in to timewindow, the psdwin is alway [0 40 2]. Is it correct? If so, what aspect of design matrix does the timewidow have effect on? thanks very much for your help. Xiaomin ___ 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] ID-swapping freesurfer data?
We don't have tools to explicitly change those strings. You can read them into matlab as Bruce suggests. You can also convert them to nifti and then back to mgz. On 08/05/2015 05:07 PM, Nate Vack wrote: Thanks! One complication I'm seeing is that when I uncompress, say, an .mgz file, the old subject number is still embedded in some text near the end of the file*. Since we want to change these ID numbers for de-identification purposes, we'd need to change them there, too. Is there a way to either strip those things or edit them? Thanks! -Nate * For example: P/studies/STUDY/DATA/mri/processed/freesurfer/IDENTIFIER/mri/transforms/talairach.xfm UNKNOWN @AutoAlign 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 mri_convert /studies/STUDY/DATA/mri/processed/IDENTIFIER/anat/T1High_native1.nii /studies/STUDY/DATA/mri/processed/freesurfer/IDENTIFIER/mri/orig/001.mgz ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/25-21:51:59-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: USER Machine: MACHINE Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 mri_convert /studies/STUDY/DATA/mri/processed/freesurfer/IDENTIFIER/mri/rawavg.mgz /studies/STUDY/DATA/mri/processed/freesurfer/IDENTIFIER/mri/orig.mgz --conform ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/25-21:54:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: USER Machine: MACHINE Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 On Mon, Aug 3, 2015 at 12:03 PM Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I think that should work without problem. On 08/03/2015 12:51 PM, Nate Vack wrote: Hi all, We're looking to change the ID system we're using for some freesurfer data. Will doing do be as simple as renaming our single-subject data directories and restarting analysis from that point, or would we need to do something more complicated? Many thanks, -Nate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 mailto: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 -- 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
Re: [Freesurfer] mri_convert IMA to MGZ
On 08/05/2015 04:24 PM, Borzello, Mia wrote: Hi freesurfers, I want to localize electrode locations from a NHP CT scan, am i able to do that with tkmedit without coregistering first? I don't need all the parcellations of a specific atlas, just the RAS coordinates. Yes Also, the CT images are IMA files. Is there a way to convert from IMA to MGZ, something like: mri_convert -i first_ct_dicom.dcm -o ct.mgz That should work I tried this and it created a file but i want to make sure i didn't need to make any specifications in the command. Thanks, m ___ 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] mkanalysis-sess, timewindow
it would be helpful to have your mkanalysis-sess command On 08/05/2015 04:17 PM, Xiaomin Yue wrote: Hi, I set timewindow to 10 in the mkanalysis-sess. When I loaded Xtmp.mat in to maltlab, then plot(flac.ev(2).Xirf), the size of the flac.ev(2).Xirf is 20 points, which is corrected because of psdwin is [0 40 2]. Should the psdwin be [0 10 2]? No matter what value I put in to timewindow, the psdwin is alway [0 40 2]. Is it correct? If so, what aspect of design matrix does the timewidow have effect on? thanks very much for your help. Xiaomin ___ 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] Fornix Segmentation
Hi everyone, So I've been going through the list trying to see if someone has encountered the same problem as me with regards to segmentation of the fornix but have not found a solution as yet. I'm a grad student and still relatively new to freesurfer. My research group is using freesurfer to segment and visualize white matter tracts in data obtained from the ADNI database. We are primarily working with the subcortical segmentation in the aseg volume. My current issue is that I am unable to find the labels for the fornix in the aseg volume; they seem to only be located in the wm volume generated by freesurfer. When I try to run mri_cc on my aseg, the corpus callosum and fornix segmentation are output together and I'm unable to analyze them separately. I'd really like all the labels I require to be contained in a single volume rather than multiple ones as that will make my job a lot easier. Is there something I'm missing? Is there a way of extracting the fornix and corpus callosum, and indeed, all white matter tracts from the same volume? Any help will be highly appreciated! Thanks in advance, Maryam ___ 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.
