Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
Looking at the image posted previously. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn I think it is pretty clear the 5.1 picture has better gray/white contrast. It is a very subtle difference, but you can see it if you look at some pieces of wm that were missed by 5.2 in this image. On Thu, Apr 11, 2013 at 12:33 PM, Yang, Daniel yung-jui.y...@yale.eduwrote: Thanks Nick! I have uploaded the relevant files to you. Thanks, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 4/10/13 1:19 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Daniel, We're repeating our paired-analysis of thickness measures between 5.1 and 5.2. In the meantime, to check for correctness, open the brain.finalsurfs.mgz file with the surfaces overlayed, and check the intensity value of the voxels which appear to be non-cortical 'black spaces', relative to neighboring gm voxels. ignore the aseg.mgz gm voxels, as those are not accurate (ie, dont load aseg.mgz when inspecting surfaces, or at least turn if off when inspecting gm regionsits still handy to see where hippocampus sits). Nick On Wed, 2013-04-10 at 11:11 +, Yang, Daniel wrote: Dear FreeSurfer Experts and Users, Did anyone find similar things using FS 5.2 (please see my previous post below)? That is, FS 5.2 is including more non-cortical black spaces within pial surfaces, compared to FS 5.1? I'm not interested in nitpicking but I feel this is a rather serious issue, so I would like to raise it again before it's completely forgotten. At the meantime I keep receiving Emails from people asking me this issue. Thanks! Daniel 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] Very different results between 5.1.0 and 5.2.0
The 5.2 image has been smoothed, by a small degree, relative to 5.1. Either prior to FS processing or by FS, it would seem. On Mon, Apr 15, 2013 at 3:29 AM, Christopher Bell christopherbell2...@gmail.com wrote: Looking at the image posted previously. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn I think it is pretty clear the 5.1 picture has better gray/white contrast. It is a very subtle difference, but you can see it if you look at some pieces of wm that were missed by 5.2 in this image. On Thu, Apr 11, 2013 at 12:33 PM, Yang, Daniel yung-jui.y...@yale.eduwrote: Thanks Nick! I have uploaded the relevant files to you. Thanks, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 4/10/13 1:19 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Daniel, We're repeating our paired-analysis of thickness measures between 5.1 and 5.2. In the meantime, to check for correctness, open the brain.finalsurfs.mgz file with the surfaces overlayed, and check the intensity value of the voxels which appear to be non-cortical 'black spaces', relative to neighboring gm voxels. ignore the aseg.mgz gm voxels, as those are not accurate (ie, dont load aseg.mgz when inspecting surfaces, or at least turn if off when inspecting gm regionsits still handy to see where hippocampus sits). Nick On Wed, 2013-04-10 at 11:11 +, Yang, Daniel wrote: Dear FreeSurfer Experts and Users, Did anyone find similar things using FS 5.2 (please see my previous post below)? That is, FS 5.2 is including more non-cortical black spaces within pial surfaces, compared to FS 5.1? I'm not interested in nitpicking but I feel this is a rather serious issue, so I would like to raise it again before it's completely forgotten. At the meantime I keep receiving Emails from people asking me this issue. Thanks! Daniel 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] nu_correct: Command not found error
I have encountered this error in the past, and I think it was because I was not sourcing SetUpFreeSurfer.sh correctly. That is the the script that sets up the MNI_DIR I think. echo $MNI_DIR or whatever it is called and it should show you if it is being setup properly. It may be pointing to the system default as you say or more likely the variable is not defined at all. On Mon, Mar 11, 2013 at 7:58 AM, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote: Sinead, In your freesurfer directory, is there an 'mni' directory? under that directory is a 'bin' directory where nu_correct should be. Nick Hi Nick, I had a look in the bin directory and there is a command called 'mri_nu_correct.mni'. Is this the command the script is trying to call? This is the only nu_correct command I could find. I specify v5.2 in the script as there are other versions installed on the clusters. Thanks again for your help! Sinead On 9 March 2013 23:23, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Sinead, Is 'nu_correct' in your freesurfer/mni/bin directory? Are you being careful to run the setup script for just freeview 5.2 and not other packages or versions which might mess-up the perl paths? Nick On Fri, 2013-03-08 at 09:50 +, Sinead Kelly wrote: Dear all, I am currently running cortical thickness analysis using Freesurfer v5.2 on a high performance computing cluster however, when I run the 'recon_all' command I get the following error Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /home/users/kellys37/CT_TEST/CON3140 Actual FREESURFER_HOME /home/support/tcin/apps/freesurfer/5.2.0 Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux nu_correct: Command not found. # #@# MotionCor Thu Mar 7 11:44:10 GMT 2013 Found 1 runs /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz /home/users/kellys37/CT_TEST/CON3140/001 mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9997, 0.0244327, -0.00148148) j_ras = (0.0239203, 0.987991, 0.152651) k_ras = (-0.00519336, -0.15257, 0.988279) Original Data has (0.898438, 0.898438, 0.9) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz... mri_add_xform_to_header -c /home/users/kellys37/CT_TEST/CON3140/001/mri/transforms/talairach.xfm /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz INFO: extension is mgz # #@# Talairach Thu Mar 7 11:44:32 GMT 2013 /home/users/kellys37/CT_TEST/CON3140/001/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 001 exited with ERRORS at Thu Mar 7 11:44:38 GMT 2013 For more details, see the log file /home/users/kellys37/CT_TEST/CON3140/001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I had did not encounter this error when using an older version of Freesurfer on our clusters. Do you know if there is any way to resolve this problem? Any advice would be appreciated. Kind regards, Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8 ___ 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
Re: [Freesurfer] parcellations to fmri space
I tried using mri_label2vol with --aparc+aseg instead of --aparc. This works and provides cortical and subcortical with no overlap. It doesn't allow me to do cortical dilation, but that is probably because it wouldn't mesh well with the subcortical ROIs. Thanks. Chris On Mon, Jul 16, 2012 at 9:03 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Chris, I don't think there is such a tool. One thing you can do is to use the aparc+aseg.mgz as the source instead of the lh and rh surfaces separately. This might solve all of your problems. doug On 07/06/2012 12:02 PM, Christopher Bell wrote: Hello Freesurfers, I have developed a pipeline that uses mri_label2vol to take freesurfer parcellations to native fmri space, and uses dilation (within mri_label2vol) to make the ROIs larger since our resolution is only 3.5x3.5x4 we would end up with only a few voxels for some ROIs due to large voxel size and partial voluming wihout the dilation. However, since the lh and rh are done separately by mri_label2vol, I now have overlap on the midline and have to go through a bunch of masking steps to eliminate it. My question is; is there a tool that will take both lh/rh parcellations to a new coordinate system, do dilation, and most importantly control for lh/rh overlap? Or any other similar suggestions. Thanks! Basically I am looking to rework my pipeline, and it seems I should be able to find a more parsimonious solution, than my Rube Goldberg approach. Chris ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] nu_correct problem
I believe this post slipped through the cracks. Anyone have any thoughts on this nu_correct error. Some subjects ran fine, so it seems to be an intermittent problem and not an installation problem. Also, is this possibly related to the avi_talairach/intensity normalization issues being discussed in another post? Chris Bell University of Minnesota On Thu, May 31, 2012 at 12:13 PM, rega0...@umn.edu wrote: Hello, I am trying to run recon-all using freesurfer 5.1.0. This worked on most of my subjects, but for about 10 subjects, I got an error: nu_correct: Command not found I can see on the archive that several others have run into this problem, but I couldn't figure out from the archives what the solution is. I do have perl installed in usr/bin. Thanks very much, Katie -- Kathryn R. Cullen, M.D. Assistant Professor University of Minnesota Medical School Department of Psychiatry Division of Child and Adolescent Psychiatry (612) 273-9825 ___ 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] wmparc
How much is the dilation (perpendicular to the cortical surface) for the creation of the white matter ROIs? Is there a citation for this? Chris Bell ___ 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] bbregister
I have run a bunch of cases through bbregister and overall it worked great! 315 out of about 325 cases the alignments were very good, but on 10 subjects it did very poorly. I can not so far find anything unusual about this data. Per earlier posts, I have tried the different initilization options with no luck. I also tried an fsl_rigid_register 6 DOF to create a starting .dat ,but that was way off too, maybe because it uses similar initilization information? I also saw the post to use --init-reg-out to save the init transform but I am not sure what to make of the output. This is aligning data that has been through the 1000FC pre-processing. This converts our RAS scans to RPI, and also de-obliques using AFNI. Would you suspect either of these steps as confusing bbregister? We are using dcm2nii (mricron) for dicom to nifti conversion. ___ 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 license file
How do I obtain a freesurfer license file? ___ 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] DODS and DOSS
Michael, Thanks for your response. It was helpful. As you suggested the thickness-age correlation group difference under DOSS is meaningless, so I have ignored that output. I am currently left with a situation where under the DOSS model I see a large ageXthickness effect (controlling for group) and a nearly identical map under the DODS model. So far so good. When I look at the group difference map, I see a large group difference for the DOSS model, and a LOT less for the DODS model. This would lead me to believe that the extra DOF in the DODS model is removing the group difference because my two groups have different ageXthickness slopes and when this is properly accounted for in the DODS model the group difference largely goes away. However, when I look at the does the thicknessXage correlation differ between groups map I see almost nothing significant? I guess my hypothesis is that the slopes are different enough between my groups to wash away the group difference, but not large enough to show up as significant? It would be nice to be able to derive some per group ageXthickness slopes from clusters or ROIS to investigate this further, is this possible? I will probably also start looking into other models, just visually looking at different vertices it appears that most of the groups difference is in the older subjects (in terms of raw thickness values) with less/none difference in younger subjects. One last aside. The demeaning of covariates still slightly confuses me. In a DOSS model it seems it wouldn't matter where you measure the intercept since both ageXthickness slopes are equal. In the DODS model, it doesn't seem to make sense to measure an intercept of two different slopes, it is more interesting to compare the slopes (in the case of different slopes you will get a different answer at every possible intercept). I am obviously a newbie to GLM and QDEC so sorry for any silly questions. Chris On Fri, Mar 4, 2011 at 1:34 PM, Michael Harms mha...@conte.wustl.eduwrote: Hi Chris, There really shouldn't be a thickness-age correlation group difference result with the DOSS model. I have FS 4.1 (rather than 5.0 on my system) but running an analogous model, I see that I do indeed get a verbal Description for such a contrast. However, if I compare that to the thickness-age correlation (accounting for group) result, I see the exact same map. And if you look at the .mat files in the contrast directory generated by qdec, you'll see that those two contrasts are identical (i.e. [0 0 1]) (or at least they are for qdec with FS 4.1). So, this appears to be a bug in the verbal descriptions that qdec provides when using a DOSS model. As to the group difference itself changing between the DOSS and DODS models, that is totally to be expected. Note that in the DODS model, whether or not you demean (center) the age variable has a critical impact on the manner in which you interpret the group contrast. cheers, -MH On Thu, 2011-03-03 at 20:41 -0600, Christopher Bell wrote: FreeSurfers, I have been analyzing my qdec data in version 5.0 and have some interesting although somewhat confusing results. Basically I have run a very simple analysis with DODS and DOSS. My discrete factor is group and my covariate is age, about as simple as can be. When I look at the results for DODS I get: thickness-age correlation (accounting for group)---result: much of brain significant group difference (I assume controlling for age, but it doesn't say explicitly)--result: one small roi significant thickness-age correlation group difference--result: one small roi spatially adjacent to group difference roi When I run DOSS I get: thickness-age correlation (accounting for group)---result: much of brain significant group difference (I assume controlling for age, but it doesn't say explicitly)--result: much of brain significant thickness-age correlation group difference--result: much of brain significant I am mostly surprised by how much larger the (group difference), and the (thickness-age correlation group difference) increase with the DOSS method. I am also not quite how to interpret the thickness-age correlation group difference in DOSS. I was thinking the DOSS method constrained both groups to have the same slope and so I was expecting to get nothing for difference in thickness-age correlation difference by group; isn't this suggesting my two groups have significantly different ageXthickness slopes even though they are constrained to have the same slope by the DOSS method? It would almost make more sense to me if the results were reversed between DOSS and DODS. If I had a large thicknessXage correlation group difference using the DODS method which allows for different slopes. Thanks for any enlightenment. Chris Bell University of Minnesota ___ Freesurfer mailing list Freesurfer
