Freesurfer September 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
200 discussions

Help on "mris_anatomical_stats"
by Lim, Lena 06 Apr '17

06 Apr '17

Dear Experts, I ran a group analysis in Qdec for the left volume and found a region of significant group difference. I wanted to extract this ROI. I defined this label and used the "map label to subjects" option in Qdec and ran the following but encountered the following error. Please kindly help... [spjwker@nanlnx2 FSL]1% mris_anatomical_stats -l lh.HCA_vol.label \-b -f PAC07/stats/lh.HCA_vol.stats PAC07 lh limiting computations to label lh.HCA_vol.label. reading volume /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/mri/wm.mgz... reading input surface /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.white... reading input pial surface /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.pial... reading input white surface /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.white... Segmentation fault Many thanks, Lena

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ExploreDTI Workshop!
by Szabolcs David 02 Apr '17

02 Apr '17

Thrilled to announce that we are going to hold an ExploreDTI workshop in Utrecht (July 4-6)! More details can be found here: http://www.exploredti.com/workshop. We hope to see you there! Cheers, Szabolcs

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Inflation of one hemi only
by Kang, XJ 10 Mar '17

10 Mar '17

Hi, I am trying to inflate right hemisphere only using the commands: recon-all -autorecon2 -hemi rh -subjid 160526 recon-all -autorecon3 -hemi rh -subjid 160526 The inflation stopped at the step: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 160526 SUBJECTS_DIR is /home/sata3/FreeSurfer/Subjects MRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white): could not open file The program "mris_volmask" needs to read "lh.white", which is not generated. Any expert has any suggestions? Maybe I didn't use the commands correctly? Thank you for your help. XJ Kang

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Cerebral (without ventricles) Volume = aseg.stats / SupraTentorialNotVent ?
by Kaiming Yin 21 Feb '17

21 Feb '17

Dear guys, Could I ask which value in the stats/aseg.stats represents the volume of the cerebrum (including the subcortical structures while excluding the ventricles and brain stem)? I'm not sure whether the "SupraTentorialNotVent" can be the value for this measurement, and could it be a bit bigger than the real value due to the partial volume effect? Besides, could I also ask is there a value represent the volume of the cerebellum? Currently I calculate the volume by adding the left/right cerebellar GM/WM values in the detailed list in aseg.stats file. Many thanks, Kaiming

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Analysis of rates or percent changes
by Katarina Trojacanec 14 Feb '17

14 Feb '17

Hi, I have a question about the analysis of rates or percent changes. I use data with available scans at baseline (TP1) and the 6-month (TP2), 12-month (TP3) and 24-month (TP4) follow-ups from ADNI dataset. An example of some of the data in the appropriate qdec table is given below: fsid fsid-base years age weight diagnosis gender Glob_CDR NPI-Q_TotScr MMSE_TotScr FAQ_TotScr visit1_2_3_4 ADNI_sub1_sc ADNI_base1 0 81.3 y AD M x x x x sc ADNI_sub1_m06 ADNI_base1 0.528767123 81.9 y AD M x x x x m06 ADNI_sub1_m12 ADNI_base1 1.030136986 82.4 y AD M x x x x m12 ADNI_sub1_m24 ADNI_base1 2.030136986 83.4 y AD M x x x x m24 ADNI_sub2_sc ADNI_base2 0 74 y AD F x x x x sc ADNI_sub2_m06 ADNI_base2 0.501369863 74.5 y AD F x x x x m06 ADNI_sub2_m12 ADNI_base2 1.005479452 75 y AD F x x x x m12 ADNI_sub2_m24 ADNI_base2 2 76 y AD F x x x x m24 The base is constructed using all four time points. The time variable is given in years. I am using long_stats_slopes for aseg.stats as follows: long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats aseg.stats --meas volume --sd $SUBJECTS_DIR --do-avg --do-rate --do-pc1fit --do-pc1 --do-spc --do-stack --generic-time --time years --stack-avg ./qdec/long_AD_NL_TP1_2_3_4 (similarly for ?h.aparc.stats) Having in mind that TP1 and TP2, as well as TP2 and TP3 are separated approximately 6 months and TP3 and TP4 are separated approximately 12 months, are the annualized percent change or atrophy rates using this scenario reasonable (statistically?). Is it maybe more reasonable to apply the same scenario using three time points (for example TP1, TP3 and TP4 from the previous example and the template based only on these time points with the same approximate difference between all of them of 12 months, or TP1, TP2 and TP3 from the previous example and the template based only on these time points with the same approximate difference between all of them of 6 months)? Best Regards, Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia

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Training Tracula to add more pathways
by Kristafor Farrant 21 Nov '16

21 Nov '16

Hi there, As a complete newbie to the Tracula tool, I have a questions about using it. Is it possible to train tracula to track additional pathways other than the 18 thats are already included? I was to track several pathways that are not included with Tracula. Best, Kris

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Getting combined bvals/bvecs
by Marissa Pifer 21 Nov '16

21 Nov '16

Hello freesurfer experts, I am trying to run tracula on subjects that have separate AP/PA direction DTI files. We combined the data into one using topup, and would now like to run tracula on the subject. The problem is, the combined file doesn't have a bvals/bvecs file. When I try to use the original bval/bvec files, I get the error that the bvals and bvecs don't match up. I have tried combining the files into one, and then running a dicom to nifty conversion to get a combined bvals/bvecs output, but that results again in two separate bvals/bvecs files as well. I then tried just have two specified bvals and bvecs. This did not give us an error message, but trac-prep took only a few seconds and did not complete the steps it was supposed to to create the directories for trac-bedp to complete. I have attached our dmrirc.example file and the log for the trac-prep step for your reference. The questions then are; is there a way to get one bvals/bvecs file that has the correct parameters for the AP and PA combined file. Or, if not, is there a way to run tracula with two sets of bvals and bvecs (one for the AP and one for the PA direction)? In case you need this information, the process is being run with freesurfer 5.3, on a macbook pro OS X version 10.9.5. Thank you in advance, Marissa

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'Invalid' license file
by Lee.Reid＠csiro.au 16 Nov '16

16 Nov '16

Hi, Our IT department have recently upgraded our cluster OS and now Freesurfer complains that its license is invalid. I have tried rebuilding, and acquiring a new license, but these do not fix the problem. The license file I am using works in my Ubuntu 12.04 computer - it has been copied across as a file, not via a text editor - and used to work on an older version of the same OS. Do you know of any solution to this issue? I've tried everything I have seen on the mailing list, including naming it .license and license.txt, checking for whitespace, etc. Our OS is now SUSE Linux Enterprise Server 12 SP1 (x86_64). Many thanks, Lee

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Mean intensity with mri_segstats : different results with .annot or .label
by Matthieu Vanhoutte 11 Nov '16

11 Nov '16

Dear experts, I am in trouble with two ways of computing mean intensity with mri_segstats. First I have used on .annot files with three different labels inside (SegId 1 to 3) : *mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot --i lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum* which give me those results: # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 1 27805 14182.6 cluster-001 8.8194 1.4351 6.2105 14.2947 8.0842 2 2 2321 1047.3 cluster-002 10.3661 1.0848 8.8375 12.9317 4.0942 3 3 552 313.1 cluster3 10.3365 0.4711 9.3719 11.8694 2.4975 Second I have created on .label files containing the three segmented labels (SegId 1 to 3) and used this label with mri_segstats: *mri_segstats --slabel fsaverage lh lh.th23.cluster.thresh1.3.label --i lh.PET.fsaverage.sm10.mgh --excludeid 0 --sum lh.pet.label.sum * which give me those results: *# ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range * * 1 1 30678 15542.9 Seg0001 8.9637 1.4701 6.2105 14.2947 8.0842 * I verified if I obtained the same results with the two ways (.annot or .label) and everything is fine comparing NVertices, Area_mm2 but Mean in first way gives me (8.8194+10.3661+10.3365)/3 = 9.84066 and with .label file Mean = 8.9637. Did I have miss anything and how is computed mean intensity ? Many thanks in advance. Best regards, Matthieu

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Multiple Comparison Question for surface-based analyses
by Ajay Kurani 28 Oct '16

28 Oct '16

Hello Freesurfer Experts, Recently there were two article published regarding clusterwise simulations for volumetric fmri analyses and potential errors for underestimating clusterwise extent thresholds. 1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes 2) biorxiv.org/content/early/2016/07/26/065862 One issue pointed out from these articles seems software specific, however the second issue is determining the proper clustersize. The heavy-tail nature of spatial smoothness seems to be ignored and a gaussian shape is generally assumed, leading to an underestimation of the spatial smoothness which can affect cluster size calculations. The issues are highlighted in the second article above. I created my own monte carlo simulation in Freesurfer for a specific brain template and I wanted to find out if these concerns also apply to my surface based simulations? I am not sure if it does since the monte carlo tool is a GRF simulation as opposed to an analytic equation, however given that these articles were highlighted very recently, I wanted to ensure I am running things appropriately for surface based cortical thickness/dti analyses. Thanks, Ajay

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Freesurfer September 2016