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30088 discussions

tkmeditParcColorsCMA
by André Ribeiro 26 Nov '13

26 Nov '13

Dear Freesurfer, Is it possible to obtain a label image with tkmeditParcColorsCMA regions, similar to aseg+aparc.mgz or aparc.a2009s+aseg.mgz ? If so how should I proceed ? Thank you in advance. Regards, Andre Santos Ribeiro

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Bad white surfaces
by Yue Cui 25 Nov '13

25 Nov '13

Hi Freesurfers: I have processed images acquired from GE Sag 3D Bravo sequence, however, the white surfaces are always messy and extend into gray matter (please see the attached example). The CNR is not bad: white = 96.0+-10.2, gray = 66.4+-18.0, csf = 38.1+-19.3 gray/white CNR = 2.053, gray/csf CNR = 1.149 lh CNR = 1.601 white = 95.8+-10.6, gray = 65.9+-18.4, csf = 36.4+-19.0 gray/white CNR = 1.985, gray/csf CNR = 1.246 rh CNR = 1.616 total CNR = 1.608 Bad white surface seems a sever problem for us, as it happens for every subject. Is it a reason of low GM/WM contrast? Does anyone have an idea about how to fix this kind of error? Thanks so much. Regards, Yue

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Re: [Freesurfer] glm_fit --prune
by Douglas N Greve 25 Nov '13

25 Nov '13

In that case, I think you will want to change the design at each voxel based on which subjects are present. I have not tried to do this with pvr, but there is no reason it should not work. To do this, create a binary volume from your data that has the 0s in it, something like mri_binarize --i y.mgh --abs --min .0000000000001 --o framemask.mgh The run mri_glmfit with --frame-mask framemask.mgh doug On 11/08/2013 01:11 PM, celine(a)nmr.mgh.harvard.edu wrote: > Thanks Doug, > Actually it is still the --pvr analysis, so I am regressing vertex by > vertex two different modalities in one group of subjects, but for one of > them, we apply a threshold to remove regions that have bad quality data. > Let me know if I am not clear! > Celine > >> you will want to use the -no-prune flag.If thisis a group analysis, you >> should be very, very careful that you know what you are doing. In >> general, setting values to 0 prior to group analysis will create biased >> results. What you really need to do is have adifferent model for each >> voxel that includes/excludes certain subjects at certain voxels. If this >> is what you want, let me know and I'll give you instructions on how to >> do it. >> >> doug >> >> >> On 11/08/2013 12:46 PM, celine(a)nmr.mgh.harvard.edu wrote: >>> Hi, >>> When using glm_fit with an input volume that has many voxels with a 0 >>> value (due to a previous thresholding for quality reasons), and the >>> voxel >>> removes might be distributed randomly across our population, is there a >>> way not to take into account those voxels in the glm_fit model? I saw >>> the >>> --pune flag, but I am not sure if it is the one to use. >>> Thanks >>> Celine >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)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(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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/

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Re: [Freesurfer] how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 groups
by Rujing Zha 25 Nov '13

25 Nov '13

Dear professor Bruce, Thanks for your attention. After recon-all, I get the cortex thickness of all subjects. Then I check the segmentations by tkmedit your_subject_name brainmask.mgz -surfs -aseg. However, my fundamental knowledge is so little that I donot know whether the quality of segmented data I can use in further analysis. That is to say, I donot know whether 3d structure of subjects is appropriate in further cortex thickness analysis. Thanks, All the best. 2013-11-25 Rujing Zha 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 发送时间：2013-11-25 22:23 主题：Re: [Freesurfer] how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 groups 收件人："Rujing Zha"<charujing123(a)163.com> 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> Hi Rujing, sorry, I don't understand. Can you clarify what you are trying to do? Bruce On Mon, 25 Nov 2013, Rujing Zha wrote: > Dear freesurfer experts, > I met a question about how to decide objectively whether I can use the > segmented data of one subkects to analyze cortex thickness between 2 groups. > Thanks. > All the best. > > 2013-11-25 > > ____________________________________________________________________________ > Rujing Zha > > _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

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curvature and its normalisation
by Koopmans, P.J. (Peter) 25 Nov '13

25 Nov '13

Dear all, Could anyone tell me how to interpret the curvature files that you can create with mris_curvature/mri_make_surfaces? The description on the website tells that the values represent something like: Value in curvature file(*.H) = 1/R, with R being the radius of a sphere tangent to the white matter surface with units in mm. It gets slightly more complicated however due to a normalisation step: In recon-all, the normalisation flag is turned on by default. To what are the values normalised? Normalising R to the local cortical thickness or something similar? Or is normalised referring to statistical procedures like a z-transform or equivalent perhaps? I am interested in the local geometry of the cortex and need to be able to interpret a value in millimetres but at the moment I don't know whether the default normalised values already are in 1/mm and without scaling or that I should re-run it without the normalise flag. Cheers Peter

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Re: [Freesurfer] How to extract a single subcortical structure from aseg+aparc.mgz file?
by Bruce Fischl 24 Nov '13

24 Nov '13

Hi Ran yes, mri_extract_label or mri_binarize --match should do the trick cheers Bruce On Sun, 24 Nov 2013, Ran Xu wrote: > Dear Freesurfer experts, > I got the aseg+aparc.mgz, and converted it into the individual T1 space. > Now, I am wondering if there is a way to extract the single subcortical > structure, like thalamus, from the converted aseg+aparc.mgz. I already know > the thalamus label, how to get thalamus.mgz file in this label. Could > someone help me out? > > Thank you very much! > > Ran > >

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Volume-defined ROI 'gone' after vol2surf
by Anita van Loenhoud 24 Nov '13

24 Nov '13

Hi all, I want to measure cortical thickness in 7 volume-defined ROIs (created in Marsbar). I followed the tutorial http://freesurfer.net/fswiki/VolumeRoiCorticalThickness. When I want to visualize my surface-based ROI after mri_vol2surf, for some reason ROI 6 and 7 do not appear in tksurfer (and with segstats, no segmentation is found). FreeSurfer does not seem to give any error message: $ mri_vol2surf --mov ~/Desktop/anita-vumc/7Rmidtempgyrus.nii --reg avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest --hemi rh --out rh.fsaverage.7Rmidtempgyrus.mgh --reshape srcvol = /home/guest/Desktop/anita-vumc/7Rmidtempgyrus.nii srcreg = avg152T1_to_fsaverage.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = 0.5 reshape = 1 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 Done loading volume Reading surface /data1/projects/ysbrand-vumc/pddatabase-freesurfer/fsaverage/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 1 using old 2 0.1 0 1 using old 3 0.2 0 1 using old 4 0.3 0 1 using old 5 0.4 0 1 using old 6 0.5 0 1 using old 7 0.6 0 1 using old 8 0.7 0 1 using old 9 0.8 0 1 using old 10 0.9 0 1 using old Done mapping volume to surface Number of source voxels hit = 21723 Reshaping 7 (nvertices = 163842) Writing to rh.fsaverage.7Rmidtempgyrus.mgh Dim: 23406 1 7 Does anyone have an idea about what might have gone wrong? Thanks!

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Re: [Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit
by Douglas Greve 23 Nov '13

23 Nov '13

Hi Clark, mri_glmfit should work fine. If you have the ROIs in a volume format (eg, nifti or mgh) you can run mri_concat on them to create a stack, then just pass the stack to mri_glmfit with the --y flag (also add --no-est-fwhm). If you don't have them in a volume format, you can create a volume format in matlab, something like mri.vol = load('yourdata.dat'); mri.vol = vol(:)'; % make sure each ROI is in a different column instead of row MRIwrite(mri,'youdata.nii'); doug On 11/22/13 5:51 PM, Clark Fisher wrote: > Hi Freesurfers, > > I am working with fsfast, and interested in doing a 2nd-level fixed effects analysis over a number of subjects. However, the volumes I'm using aren't in a standard freesurfer space (native, talraich, etc.). They are nx1x1 volumes containing results from n ROIs. While I got first level analysis in fs-fast working, I don't think I'll get mri_glmfit to work in this space. > > What is the math that mri_glmfit carries out to do the fixed-effects analysis? Based on the inputs, it seems to rely upon the variance and degrees of freedom from each individual subject, and I can't find a formula in the general MRI literature (or in the freesurfer group analysis presentation) that uses both of these in a fixed-effects analysis. > > Thanks, > Clark > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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LONG stream question {Disarmed}
by Kirov, Ivan 22 Nov '13

22 Nov '13

Dear FreeSurfer group/Dr. Reuter, My questions are in regards to the LONG stream. My version is: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 1) Error message During the creation of the BASE, I get the following error in the beginning of the recon: >>>WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s.<<<< What should I be aware of in regards to this error? The images were all acquired using the same MPRAGE protocol. All timepoints were fed MPRAGEs reconstructed in the axial orientation, but some may have been reconstructed at an angle. I was assured that this is not an issue for FreeSurfer, but could this be the reason for the error? 2) Conversion of LONG run aseg.mgz segmentations to native anatomical space Executing the commands for converting aseg.mgz to native space (http://freesurfer.net/fswiki/FsAnat-to-NativeAnat<http://freesurfer.net/fswiki/FsAnat-to-NativeAnat>) in the folder of a long run (me1.long.me_base) does not convert. It seems to me that (unlike the cross runs) the long runs are all in the same space (in the template/ base space?) and their rawavg.mgz does not match that of the corresponding cross run. Some insight on this would be appreciated. The question is how to convert an individual long run's aseg.mgz into native anatomical space. Perhaps using the rawavg.mgz from the corresponding cross run? Thank you very much! Ivan -- Ivan Kirov, PhD Postdoctoral fellow New York University School of Medicine Center for Biomedical Imaging 660 1st Ave, 4th floor, New York, NY 10016 Tel: 212-263-3337 Fax: 212-263-7541 ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================

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TRACULA exists uncompleted
by Emad Ahmadi 22 Nov '13

22 Nov '13

Hello, I'm using TRACULA for analyzing a number of cases, and I've made a file to successively run the three stages of pre-processing, model fitting, and pathways reconstruction which is attached (ter1.tcsh). I've also attached the configuration file I'm using (dmrircTer1.cshell). The problem is that TRACULA exists uncompleted. I've attached the log files. I'd really appreciate it if you let me know where I'm making some sort of a mistake. All the best, Emad

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