[Freesurfer] DODS vs DOSS for correlation analysis
Hi Doug, I am carrying out some correlations between cortical thickness and cognitive ability, and had a question about the use of DODS vs DOSS for my analysis with Qdec. From reading some of the forums, it seems as though DOSS should be used when there are no interactions present. I am including gender as a covariate (fixed factor) and age as a nuisance variable in my model. When I run this with DODS, it shows that the correlation between thickness and cognition does not differ between males and females - does this mean that I should run the correlation using DOSS? I only seem to find significant correlations using DOSS, however I do not want to report these if the analysis is not correct. Thanks, Cassie Cassandra Wannan *PhD Candidate/Research Assistant/Psychology Tutor* Melbourne Neuropsychiatry Centre 0433 339 839 cwan...@student.unimelb.edu.au ___ 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 vs DOSS for correlation analysis
Hi Doug, I'm using version 5.3. I had read about the bug but the release notes for 5.3 didn't mention not using DOSS in Qdec, so I thought the issue must have been resolved. If not, I'll let my colleagues know as I believe some of them are still using DOSS in Qdec. Cheers, Cassie ___ 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] Different significant clusters: qdec vs mri_glmfit-sim
Hi Freesurfer experts, Qdec does not appear to allow me to automatically extract mean values for significant clusters for each participant, so I have been doing this using command line after running the original analysis in Qdec. However, I have found that there are some differences in the significant clusters between the two. The command line I am using is: mri_glmfit-sim --glmdir TRSCtrl_Vocab_DODS --cache 2 abs --cwp 0.01 I believe that this should correspond to analysis in Qdec using the preset threshold of 2 and Monte-Carlo Null-Z Simulation value of 2.0 (0.01). The significant clusters from Qdec are: # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZCWP CWPLowCWPHi NVtxs Annot 17.740 109023669.23 -6.1 -12.5 47.0 0.00120 0.00080 0.00170 1618 paracentral 25.854 63055 1542.69-19.0 -73.2 -3.6 0.00010 0.0 0.00020 1913 lingual 35.393 127437 1063.38-23.4 -6.9 -28.0 0.00010 0.0 0.00020 2069 entorhinal 45.026 112833788.05-13.9 -45.3 38.9 0.00010 0.0 0.00020 1660 precuneus 54.726 141529523.23-34.4 -5.7 10.9 0.00760 0.00650 0.00870 1456 insula 64.413 23898863.24-13.4 25.1 26.4 0.00010 0.0 0.00020 1495 superiorfrontal 73.819 21492874.38-17.8 -72.7 29.0 0.00010 0.0 0.00020 1321 precuneus Whereas from the command line: # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWP CWPLowCWPHi NVtxs Annot 17.740 109023668.36 56.9 -11.3 35.0 0.00050 0.00020 0.00080 1618 postcentral 25.854 63055 1328.30 52.2 -58.3 -8.8 0.00010 0.0 0.00020 1913 inferiortemporal 35.393 127437 1004.26 32.5 -2.8 -38.4 0.00010 0.0 0.00020 1950 fusiform 45.026 112833782.44 54.3 -41.2 42.3 0.00010 0.0 0.00020 1660 supramarginal 54.413 23898780.09 56.52.16.1 0.00010 0.0 0.00020 1495 precentral 63.819 21492673.28 46.3 -59.1 31.8 0.00050 0.00020 0.00080 1321 inferiorparietal When I view the glmfit clusters in free view they do appear very similar to the ones in Qdec, but there is one less significant clusters and obviously the cluster names are different. Am I using the correct command line to extract this information? Many thanks, Cassie ___ 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] Hippocampal subfield segmentation with T1 and T2
Hi all, I've been trying to run the hippocampal subfield segmentation with T1 and T2 images, and haven't had much luck. I had previously run recon-all on all my scans in v5.3, but testing on one subject I re-ran recon-all with the additional T2 scan, and that seems to have run fine. However, when I try to run the subfield segmentation, I am getting errors. My command line is: recon-all -s CRC040 -hippocampal-subfields-T1T2 CRC040/mri/T2.mgz CRC040T1T2 -no-isrunning but I have also tried: recon-all -s CRC040 -hippocampal-subfields-T1T2 CRC040/mri/orig/T2raw.mgz CRC040T1T2 -no-isrunning and: recon-all -s CRC040 -hippocampal-subfields-T1T2 ./CRC040.nii CRC040T1T2 -no-isrunning The error I am getting is: /Applications/freesurfer_v6/bin//mri_robust_register --mov /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/norm.mgz --maskmov /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//wholeBrainMask.mgz --dst /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/T2.mgz --lta /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/transforms/T1_to_CRC040T1T2.v10.lta --noinit --cost NMI -nosym >/dev/null: Signal 127 ERROR: cannot find transform file /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/transforms/T1_to_CRC040T1T2.v10.lta gunzip: can't stat: /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//T2resampledLikeT1.mgz (/data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//T2resampledLikeT1.mgz.gz): No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in segmentSubjectT1T2_autoEstimateAlveusML (line 192) MATLAB:badSwitchExpression Any idea what could be causing the issue? The hippocampal pipeline runs fine without the T2 scan, however I am planning to use the subfield segmentation as a mask for some white matter tractography analysis in FSL, and the dimensions of the output are not close to my nifti files. I was hoping that using the T2 registration would help with this, but can't get it to work! Any help would be greatly appreciated. Kind regards, Cassie ___ 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.
