[Freesurfer] Other things to consider when setting -min_border_white -min_gray_at_white_border?
Dear Bruce and Freesufers, Adding to our previous discussion. You managed to fix a very bad segmentation by setting some expert options (mri_normalize -gentle and setting a fixed level for -min_border_white -min_gray_at_white_border). It was a very nice recovery of, what I thought to be, a hopeless image. As I in my project have around 800 images I was also testing these options on 10 more images that you used to recover the bad image. The test on the 10 other images (that also worked well without expert options) was quite good. The segmentation looked ok. What I am wondering now is if there is other aspects to consider when setting fixed levels in mris_make_sufaces? As I told you I looked into the recon-all log file and found that when FS is running normally in creates different levels of -min_border_white -min_gray_at_white_border for each image. As this is the Normal way for FS to run I suppose that this is the optimal way to run. So what is the disadvantages of setting fixed levels for -min_border_white -min_gray_at_white_border? Thanks! Erik ___ 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] Number of pixel count
yes, but recon-all will run it for you and store the results in text files in each subject's stats dir On Fri, 14 Feb 2014, Saurabh Thakur wrote: Hi Bruce, That means i should use mri_segstats for the same? Thanks, cheers Saurabh Thakur, On Wed, Feb 12, 2014 at 6:52 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Saurabh we don't measure sulcal CSF as it's really not visible on only a T1. The other measures should all be in the files in the stats directory - no need to measure it yourself. cheers Bruce On Wed, 12 Feb 2014, Saurabh Thakur wrote: Hello Free surfer Expert , I am kooking for the exact value of voxel / pixel which represent White ,Grey and CSF fluid matter in brain. I am trying to draw contour, and to measure the count...or How to count the pixel for particular region...? Thanks in advance for your timely advise. cheers Saurabh Thakur, 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] Other things to consider when setting -min_border_white -min_gray_at_white_border?
Hi Erik we try very hard to accomodate a wide variety of T1-weighted MRI sequences with extremely variable contrast properties. That piece of code tries to estimate and adapt to the contrast it finds in the image, but things like subjeect motion can mess it up. If you have a fixed acquisition with known contrast properties then there should be no problem with simply telling recon-all what to expect instead of having it discover it on its own cheers Bruce On Fri, 14 Feb 2014, Erik Lindberg wrote: Dear Bruce and Freesufers, Adding to our previous discussion. You managed to fix a very bad segmentation by setting some expert options (mri_normalize –gentle and setting a fixed level for -min_border_white -min_gray_at_white_border). It was a very nice recovery of, what I thought to be, a hopeless image. As I in my project have around 800 images I was also testing these options on 10 more images that you used to “recover” the bad image. The test on the 10 other images (that also worked well without expert options) was quite good. The segmentation looked ok. What I am wondering now is if there is other aspects to consider when setting fixed levels in mris_make_sufaces? As I told you I looked into the recon-all log file and found that when FS is running normally in creates different levels of -min_border_white -min_gray_at_white_border for each image. As this is the Normal way for FS to run I suppose that this is the optimal way to run. So what is the disadvantages of setting fixed levels for -min_border_white -min_gray_at_white_border? Thanks! Erik ___ 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: Tracula Error: bvecs and bvals don't have the same number of entries
Hi Francesco - It looks like you haven't defined SUBJECTS_DIR in your configuration file. That needs to be set to the directory where the freesurfer recons of your subjects' T1 scans can be found. For more info, check the example configuration file, $FREESURFER_HOME/bin/dmrirc.example, or the tracula tutorial. Hope this helps, a.y On Fri, 14 Feb 2014, Francesco Baldacchini wrote: Hi Anastasia, I've just rerun trac-all path and got the same error. In attach there is the trac-all.log. Thanks, Francesco Baldacchini 2014-02-13 20:30 GMT+01:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Francesco - Please attach your trac-all.log file. There may be an error at an earlier stage that's causing this error. Thanks, a.y On Thu, 13 Feb 2014, Francesco Baldacchini wrote: Hi Anastasia, Thank you for the help, finally I discovered the cause of the problem. The language of the system was set to Italian which use the comma as a decimal separator instead of the dot. So I was able to run the trac-all but I encountered another problem. The error I'm getting is the following: #@# Priors Thu Feb 13 17:33:25 CET 2014 /usr/local/freesurfer/bin/dmri_train --outdir /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.Beal.2838.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni/lowb_brain_mask.bb r.nii.gz --fa /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dtifit_FA.nii.gz --cptdir
[Freesurfer] tkmedit and masking
Hello, I am using tkmedit to display functional data as an overlay on anatomical data. I am asking myself if there is a feature in tkmedit which allows to apply a mask to the functional. Ideally would be a cortex mask to remove all non-cortex voxels. Regards Joerg -- Joerg Pfannmoeller pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FDR question
I see. Thanks for your input! Panos This kind of thing can happen, especially when there is not much activity in the map doug On 02/11/2014 12:02 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug and Martin, Thanks both for your replies! Doug, I would normally set the FDR to something close to .05 but when this value didn't give me any significant clusters for my analysis, I was trying to find which value was the min one that gave significant clusters just out of curiosity, and this value happened to be 0.88. But I wasn't going to actually use this value for my analysis. It just surprised that for such a high fdr threshold, the min -log(p) value increased so much, hence excluding every uncorrected significant cluster for any fdr threshold less than 0.88. Best, Panos Hi Panos, also the LME tools (matlab) have tools for FDR correction: /lme_mass_FDR/ (Original Benjamini and Hochberg FDR procedure) /lme_mass_FDR2/ (A more powerful two-stage FDR procedure: Adaptive Linear Step-up Procedures that control the False Discovery Rate Benjamini, Krieger, Yekutieli ) Best, Martin On 02/10/2014 03:28 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS community, I was wondering if anyone had a chance to give this a look. Thanks in advance, Panos Hi FS community, I am doing a cortical thickness comparison between a diseased and a healthy group. After running the mri_glmfit command for both hemispheres, I project the uncorrected significance map and there are a number of significant clusters showing (if you consider the p value to be at most 0.05). However, instead of using the clusterwise Correction for Multiple Comparisons, I wanted to use FDR to see what the results would look like, and I had a few questions regarding the whole process: 1) Are Tksurfer and QDEC the only tools in FS that I can apply the FDR correction with, or are there any other ways? 2) In Tksurfer, I tried using the Set Threshold Using FDR tool, and when I set the rate from 0.88 to 0.87 it bumps up the minimum threshold from 1.37 to 3.24 hence resulting in no significant clusters for rates less than 0.88. Does that sound normal? Thanks in advance! Panos ___ 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 -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] BVECS and BVALS file
Hi Anastasia: Hope all is well. I have DTI data for 65 brains. They are in nifti format. However, they do not have the bvecs and bvals information. I searched the web but they only have the conversion information for dicom files. I opened the header on MRICRON but how does one convert these values into table form. thanks so much, Alan Martinos Center. ___ 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] BVECS and BVALS file
Hi Alan - The gradient table is not saved in the nifti header. Are you using a standard MGH diffusion sequence? a.y On Fri, 14 Feb 2014, Alan Francis wrote: Hi Anastasia: Hope all is well. I have DTI data for 65 brains. They are in nifti format. However, they do not have the bvecs and bvals information. I searched the web but they only have the conversion information for dicom files. I opened the header on MRICRON but how does one convert these values into table form. thanks so much, Alan Martinos Center. ___ 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] recon-all pial reconstruction error
Hi Rujing It looks to me like there is a bunch of anterior temporal wm that is missed, either because of a bias field or lack of myelination if it is a kid or a disease. Try putting some control points in the wm and see if that fixes things. Usually the pial surface being wrong is because the white is wrong. cheers Bruce On Feb 14, 2014, at 10:32 PM, charujing123charujing...@163.com wrote: Hi FS experts, After running the recon-all -s CON_EIU12, I found some inappropriate error in pial reconstruction, which can be got in the attachment. I knew how to remove voxels from GM areas. But I did not know how to add some voxels into GM area in this case. Thanks. All the best. Rujing Zha 2014-02-15 charujing123 111.jpg ___ 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] recon-all pial reconstruction error
Hi Bruce, Thanks Bruce. I see. I will try. All the best. Rujing Zha 2014-02-15 charujing123 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2014-02-15 12:26 主题：Re: [Freesurfer] recon-all pial reconstruction error 收件人：charujing123charujing...@163.com 抄送：freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Hi Rujing It looks to me like there is a bunch of anterior temporal wm that is missed, either because of a bias field or lack of myelination if it is a kid or a disease. Try putting some control points in the wm and see if that fixes things. Usually the pial surface being wrong is because the white is wrong. cheers Bruce On Feb 14, 2014, at 10:32 PM, charujing123charujing...@163.com wrote: Hi FS experts, After running the recon-all -s CON_EIU12, I found some inappropriate error in pial reconstruction, which can be got in the attachment. I knew how to remove voxels from GM areas. But I did not know how to add some voxels into GM area in this case. Thanks. All the best. Rujing Zha 2014-02-15 charujing123 111.jpg ___ 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.
