[Freesurfer] nii format input for recon-all
Dear all, I have done the recon-all for DICOM format input of all subjects. Part of subjects extracted brain volume not very perfectly. I want to use brain volumes nifti format which have strip the skull and neck well. My question is how to use the brain volume in nii format to segment and next recon-all analysis. Thanks. All the best. 2013-11-29 Rujing Zha___ 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] glmfit error
Dear FS experts I'm running glmfit with FS v5.1 and get the following error:ERROR: matrix is ill-conditioned or badly scaled, condno = 1.75146e+07Possible problem with experimental designcommand line:mri_glmfit --surf PLI_MCI_sample7_avg lh --C /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/contrast_withinE4_neg.mat --fsgd /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/lh.cortex_AVGthickness_APOB_fsgd.txt dods --label /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/label/lh.cortex.label --y /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/lh.thickness_s12mm.mgh --no-prune --glmdir /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/resultsthickness_cortex_s12mm_BiomrkrsWithin/lh.cortex_AVGthickness_APOB_contrast_withinE4_neg/I've performed analyses like this many times, but with different subjects, more subjects but same fsgd structure (same regressors), and I have no Idea of what's wrong in here.Please, find attached the contrast and the fsgd matrices used.Can any one guide me on this?Many thanks in advanced,Gabriel contrast_withinE4_neg.mat Description: Binary data GroupDescriptorFile 1 Title PVEc-PET_with_MRI in sig_clusters of MC_3000 Class E4female Class E4male Class noE4female Class noE4male variables zAge zAPOB zlh.cortex_AVGthickness Input mci_01_year1 noE4male -0.025380 -0.495746 -0.569553 Input mci_02_year1 noE4male 0.416237 -0.163064 -1.388804 Input mci_04_year1 noE4female -0.466997 -1.018533 1.324541 Input mci_10_year1 noE4male -0.319792 -1.351215 0.286936 Input mci_11_year1 noE4female 0.563442 -0.400694 -0.384206 Input mci_14_year1 noE4male -0.466997 -0.281879 0.611082 Input mci_15_year1 noE4female 1.152265 -0.567035 0.446893 Input mci_16_year1 noE4male 0.857854 0.549827 -1.563149 Input mci_20_year1 noE4male -0.614203 -1.066059 -0.254717 Input mci_23_year1 noE4male 1.299471 -0.780902 -0.043134 Input mci_25_year1 noE4male -0.761409 -0.899718 0.469744 Input mci_33_year1 noE4male -0.908614 0.858747 0.584846 Input mci_36_year1 noE4male -0.025380 2.260766 -0.997798 Input mci_38_year1 noE4male -2.822288 2.759790 1.354163 Input mci_39_year1 noE4male -1.350231 2.569685 0.621238 Input mci_06_year1 E4female -0.172586 -0.234353 -0.633028 Input mci_07_year1 E4male -1.350231 -0.139301 -0.126075 Input mci_08_year1 E4female -0.025380 0.383486 -1.171297 Input mci_09_year1 E4female 0.857854 -0.234353 -0.370665 Input mci_13_year1 E4male 0.121825 -0.495746 0.904760 Input mci_17_year1 E4male -0.466997 -0.044248 -0.776059 Input mci_18_year1 E4female 1.005059 -0.163064 -0.820915 Input mci_19_year1 E4male 1.152265 0.074567 -2.081952 Input mci_21_year1 E4female 0.121825 -0.091774 1.423562 Input mci_27_year1 E4female -1.350231 -0.543272 2.172568 Input mci_29_year1 E4male 1.888294 0.240908 0.683020 Input mci_35_year1 E4male 0.710648 -0.567035 1.014783 Input mci_41_year1 E4female 0.269031 0.169619 -0.510310 Input mci_42_year1 E4male 0.710648 -0.329405 -0.206476 ___ 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] Cortical thickness/surface area in volume-defined ROIs
Dear Freesurfer experts, I want to use volume-defined ROIs (obtained in a VBM study) to extract mean thickness and surface area, in a total group of 138 participants. I followed the tutorial 'Cortical Thickness of a volume-defined ROI'. I have a few questions regarding this analysis: 1. The volume-defined ROI (i.e. orange dot) appears normal on my avg152_T1 and fsaverage. After the vol2surf-step, however, a few problems arise. The new ROIs look very different: one ROI actually consists of two clusters close to each other, one is very small and two ROIs have completely disappeared. Does anyone know why this happened? 2. When I want to obtain surface area data instead of thickness data, is it sufficient to replace 'thickness' with 'area' in the surf2surf command (it seems to work, but I want to check)? So: --sval lh.area \ --tval lh.area.fsaverage.mgh \ 3. mri_segstats creates separate files for each ROI in each participant. When I want to have all thickness and area ROI data in one file, can I use asegstats2table, meas mean (it seems to work, but I want to check)? Any help would be very much appreciated! Anita ___ 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] Cortical thickness/surface area in volume-defined ROIs
Dear Anita, Would you please tell me where I can find Cortical Thickness of a volume-defined ROI? Thanks, All the best. 2013-11-29 Rujing Zha 发件人：Anita van Loenhoud acvanloenh...@gmail.com 发送时间：2013-11-29 21:51 主题：[Freesurfer] Cortical thickness/surface area in volume-defined ROIs 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Dear Freesurfer experts, I want to use volume-defined ROIs (obtained in a VBM study) to extract mean thickness and surface area, in a total group of 138 participants. I followed the tutorial 'Cortical Thickness of a volume-defined ROI'. I have a few questions regarding this analysis: 1. The volume-defined ROI (i.e. orange dot) appears normal on my avg152_T1 and fsaverage. After the vol2surf-step, however, a few problems arise. The new ROIs look very different: one ROI actually consists of two clusters close to each other, one is very small and two ROIs have completely disappeared. Does anyone know why this happened? 2. When I want to obtain surface area data instead of thickness data, is it sufficient to replace 'thickness' with 'area' in the surf2surf command (it seems to work, but I want to check)? So: --sval lh.area \ --tval lh.area.fsaverage.mgh \ 3. mri_segstats creates separate files for each ROI in each participant. When I want to have all thickness and area ROI data in one file, can I use asegstats2table, meas mean (it seems to work, but I want to check)? Any help would be very much appreciated! Anita___ 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] Cortical thickness/surface area in volume-defined ROIs
Hi Rujing Zha, Click this link: http://freesurfer.net/fswiki/VolumeRoiCorticalThickness Anita ___ 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] Cortical thickness/surface area in volume-defined ROIs
Hi Anita the problem is that the cortex is not well aligned in the avg152 space, and so a volume-defined ROI will not follow the contours of the cortex well. Not sure that there's much you can do about this except possibly map the ROI back to the individual subjects, and recreate it in fsaverage space using surface-based tools. Perhaps Doug will chime in after the trytophan wears off Bruce On Fri, 29 Nov 2013, Anita van Loenhoud wrote: Dear Freesurfer experts, I want to use volume-defined ROIs (obtained in a VBM study) to extract mean thickness and surface area, in a total group of 138 participants. I followed the tutorial 'Cortical Thickness of a volume-defined ROI'. I have a few questions regarding this analysis: 1. The volume-defined ROI (i.e. orange dot) appears normal on my avg152_T1 and fsaverage. After the vol2surf-step, however, a few problems arise. The new ROIs look very different: one ROI actually consists of two clusters close to each other, one is very small and two ROIs have completely disappeared. Does anyone know why this happened? 2. When I want to obtain surface area data instead of thickness data, is it sufficient to replace 'thickness' with 'area' in the surf2surf command (it seems to work, but I want to check)? So: --sval lh.area \ --tval lh.area.fsaverage.mgh \ 3. mri_segstats creates separate files for each ROI in each participant. When I want to have all thickness and area ROI data in one file, can I use asegstats2table, meas mean (it seems to work, but I want to check)? Any help would be very much appreciated! Anita ___ 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] Cortical thickness/surface area in volume-defined ROIs
Dear, I get it. Thanks. All the best. 2013-11-29 Rujing Zha 发件人：Anita van Loenhoud acvanloenh...@gmail.com 发送时间：2013-11-29 22:18 主题：Re: [Freesurfer] Cortical thickness/surface area in volume-defined ROIs 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Hi Rujing Zha, Click this link: http://freesurfer.net/fswiki/VolumeRoiCorticalThickness Anita___ 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] major lobes
Hi all, Since I haven't heard back about my question so far, I'm posting it again! Sorry about this but I really need your help! As mentioned in my previous posts, I'm interested in having the GM volumetric lobar masks (frontal, parietal, temporal, occipital, and insular) with the final goal of moving them the DTI space to perform thalamic parcellation. I've ran the following commands: 1- a. mri_annotation2label --subject P2 --hemi lh --lobesStrict freeSurfer_Results/P2/label/lh.freeSurfer_lobes.annot b. mri_annotation2label --subject P2 --hemi rh --lobesStrict freeSurfer_Results/P2/label/rh.freeSurfer_lobes.annot 2- mri_aparc2aseg --annot freeSurfer_lobes --s P2 --o freeSurfer_Results/P2/label/freeSurfer_lobes.nii.gz I thought after doing this I'm going to get the 5 or 6 lobar labels, but instead I'm getting a detailed WM + GM segmentation. I looked at FreeSurferColorLUT.txt and tried to manually combine labels in the range of 1000-1035 for the left and 2000-2035 for the right hemisphere to get the lobe masks, but after having a closer look I realised that labels 1002,1008-1035 2002,2008-2035 are all empty (ie. I only have 7 labels in each hemisphere)! so, I'm now not sure how to manually combine these labels either! Could someone PLEASE PLEASE clarify this for me! I would really appreciate any help! Thanks, -Mojdeh ___ 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] major lobes
The commands look right and it sounds like you might have the right result. What do you mean you are getting a detailed WM + GM segmentation? If you just load freeSurfer_lobes.nii.gz into tkmedit, the label names will be all messed up because you don't have the proper color table, but you should still only get 7 per hemi. To get the proper color table, run mri_annotation2label with --ctab, then merge the two ctabs you get (lh and rh). You don't need to rerun mri_aparc2aseg doug On 11/29/13 3:09 PM, Mojdeh Zamyadi wrote: Hi all, Since I haven't heard back about my question so far, I'm posting it again! Sorry about this but I really need your help! As mentioned in my previous posts, I'm interested in having the GM volumetric lobar masks (frontal, parietal, temporal, occipital, and insular) with the final goal of moving them the DTI space to perform thalamic parcellation. I've ran the following commands: 1- a. mri_annotation2label --subject P2 --hemi lh --lobesStrict freeSurfer_Results/P2/label/lh.freeSurfer_lobes.annot b. mri_annotation2label --subject P2 --hemi rh --lobesStrict freeSurfer_Results/P2/label/rh.freeSurfer_lobes.annot 2- mri_aparc2aseg --annot freeSurfer_lobes --s P2 --o freeSurfer_Results/P2/label/freeSurfer_lobes.nii.gz I thought after doing this I'm going to get the 5 or 6 lobar labels, but instead I'm getting a detailed WM + GM segmentation. I looked at FreeSurferColorLUT.txt and tried to manually combine labels in the range of 1000-1035 for the left and 2000-2035 for the right hemisphere to get the lobe masks, but after having a closer look I realised that labels 1002,1008-1035 2002,2008-2035 are all empty (ie. I only have 7 labels in each hemisphere)! so, I'm now not sure how to manually combine these labels either! Could someone PLEASE PLEASE clarify this for me! I would really appreciate any help! Thanks, -Mojdeh ___ 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] how to recon-all multiple participants simultaneously? thanks
Dear Freesurfers, I'd like to ask how could we recon-all multiple participants at the same time? My laptop has a 32G ram and a 8-core-intel-Core-i7 CPU, i expect it could speed up the surface construction by running several participants simultaneously. When i use the following command: 'foreach i (1 2 3);recon-all -subjid sub$i -all -openmp8;end', each participant needs 4-5 hours. Although this is much faster than the typical time consumption as stated in freesurfer wiki, i notice only 3 out my 32G working memory is used under such command. So I am wondering if there are some other ways to make full use of the working memory and make the surface construction go even faster. I have tried to open 8 terminal windows, each for a separate participant, and for each window, the command was like this, 'recon-all sub01 -all openmp 8'. It turned out the analysis ran extremely slow, none of the subjects finished even after 36 hours, the CPU was 100% used, but still no more than 7 of the 32G working memory was occupied. So, question, is it possible for me to make the analysis more quickly, and if so, how？ Looking forward to your informations, and thank you a lot! Chen ___ 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.
