Freesurfer

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30076 discussions

Removal from Mailing list
by Haniya Saleh 28 Mar '22

28 Mar '22

External Email - Use Caution Hello, Can I please be removed from this mailing list? I no longer work in a position related to freesurfer. Thanks! Warm Regards, Haniya Saleh ________________________________________________ Haniya Saleh | OVC IT Technician - Client Productivity Ontario Veterinary College (OVC) | University of Guelph MacNabb House rm. 103 | 2 College Avenue West | Guelph, ON | N1G 2W1 519-824-4120 x54691 | hsaleh(a)uoguelph.ca

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Re: [Freesurfer] Pass code to expand the archive of Free surfer 7.2.0
by fsbuild 28 Mar '22

28 Mar '22

External Email - Use Caution Hello Krystaly, Sending the info to your email shortly. - R.On Mar 28, 2022, at 01:15, krystaly <krystaly(a)hku.hk> wrote:        External Email - Use Caution        Dear Free Surfer expert,Would you please send me the pass code for opening the archive of FS 7.2.0?Thanks for your attention!Yours sincerely,Krystal_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Pass code to expand the archive of Free surfer 7.2.0
by krystaly 28 Mar '22

28 Mar '22

External Email - Use Caution Dear Free Surfer expert, Would you please send me the pass code for opening the archive of FS 7.2.0? Thanks for your attention! Yours sincerely, Krystal

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lh.pial and rh.pial is 0Kb, I cannot open them by using freesurfer
by Muhammed Görünen 27 Mar '22

27 Mar '22

External Email - Use Caution Hi, I run recon-all process for a subject's T1 data. At the end, the pial files are 0Kb and I cannot open them from python. What would be the problem here? Also, is there any difference between pial file and pial.T1 file? I will be happy if you can answer. Best, --Muhammed

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classes for GLM analysis
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 27 Mar '22

27 Mar '22

External Email - Use Caution Hi all, I am doing an analysis and generating the FSGD. I understand sex and race are classes in this context, but something I was also hoping to regress out is the effects of scanner/sequences. We have a large participant size, so we have around 10+ scanner/sequences, which makes for a large amount of classes combinations, with some having just 1 (if not zero) fitting into a class. Would you proceed with this nonetheless? If not, should scanner/sequence be something that we consider? Should we find some other way to adjust site (I don't think we can z-score...). Or can we consider site/scanner as a continuous variable Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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Question about calculation of pial area in DKatlas
by Dongyue Zhou 27 Mar '22

27 Mar '22

External Email - Use Caution Dear FreeSurfer experts: I want to calculate mean pial surface area in DKatlas in individual space.And I know the function read_annotation.m in $FREESURFER_HOME/matlab for loading this atlas.And if I can load sub/surf/?h.area.pial as the area in each vertice and calculate mean pial area by dividing sum PSA of all vertices in one ROI by the number of vertices in this ROI?But why my result is not the same as result in sub/stats/?h.aparc.stats ? Does the column named surface area represent mean PSA in each ROI?

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mri_vol2vol anatomical to functional
by Manenti, Giorgio 27 Mar '22

27 Mar '22

External Email - Use Caution Dear Freesurfer experts, I am getting problems to transform my xh.ribbon.mgh from anatomical 256x256x256 to functional 104x104x69 space. When converting the ribbon via “ mri_vol2vol —reg REGfile —mov INPUT —targ funcTEMPLATE —o OUTPUT “ and checking via freeview, i am getting the right functional space dimensions but the INPUT and OUTPUT .mgz are never overlapping. Why am i getting this misplacement ? Is this problem due to the register file i provide or maybe it is just a visualisation error (perhaps freeview is not the best way to check the conversion). I tried to change REGfile by providing the 1) init.register.dof6.dat and 2) register.dof6.lta (changing “—reg with —lta”). I am getting an almost perfect merge when using the .lta file but still the two volumes are misaligned. I tried mri_label2vol as well, but as expected i got worse results. To provide a minimum more detail, after recon-all i process the anatomy with the longitudinal recon. At that point i use the longitudinal anatomy to register the functional data, which i process by 1) mk-template 2) topup & applytopup. Many thanks in advance Warm regards Giorgio

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mri_segment_hypothalamic_subunits error: Illegal instruction 4
by Alice Tao 27 Mar '22

27 Mar '22

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to use the mri_segment_hypothalamic_subunits tool on subjects that have been analyzed with recon-all as described on the wiki page (https://secure-web.cisco.com/1pXzYS0fndek4-BNAZ4GmvKEawRrGwFtSNJa-z80qhPYpZ…) but I received the following error when I run the mri_segment_hypothalamic_subunits command (mri_segment_hypothalamic_subunits--s): Illegal instruction: 4 Does anyone have any suggestions on how to trouble-shoot this problem? recon-all does not seem to have any issues. 1) FreeSurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b 2) Platform: macOS Monterey, version 12.2.1 Thank you! Alice

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qdec analysis error
by David 27 Mar '22

27 Mar '22

External Email - Use Caution Hello FreeSurfer Developers, I have a problem. Can you help me freesurfer version : 6.0.0 Load qdec when I run qdec.table.dat, the data is loaded correctly, but when I design, I choose discrete and continuous factors for analysis The error log is as follows ： ———————————————— Input table: /media/root/Backup_Plus2/new/RECON/qdec/qdec5.table.dat Subj#, SubjID, Data... 1 bd1 d Male 15.000000 8.000000 2 bd2 d Female 19.000000 13.000000 3 bd3 d Male 25.000000 9.000000 4 bd4 d Male 17.000000 12.000000 5 bd5 d Male 16.000000 10.000000 6 bd6 m Female 22.000000 12.000000 7 bd7 d Male 17.000000 11.000000 8 bd8 d Female 19.000000 13.000000 9 bd9 m Female 26.000000 7.000000 10 bd10 m Male 53.000000 15.000000 11 bd11 m Female 56.000000 4.000000 12 bd12 d Female 21.000000 14.000000 13 bd13 m Female 19.000000 12.000000 14 bd14 m Female 32.000000 15.000000 15 bd15 d Male 21.000000 9.000000 16 bd16 d Male 16.000000 10.000000 17 bd17 d Male 15.000000 11.000000 18 bd18 d Female 32.000000 10.000000 19 bd19 d Female 20.000000 15.000000 20 bd20 d Female 17.000000 11.000000 21 bd22 m Male 22.000000 11.000000 22 bd23 m Female 28.000000 6.000000 23 bd24 d Male 26.000000 11.000000 24 bd25 m Female 24.000000 9.000000 25 bd26 m Female 30.000000 6.000000 26 bd27 m Female 20.000000 12.000000 27 bd28 d Female 28.000000 16.000000 28 bd29 m Female 18.000000 12.000000 29 bd30 d Male 21.000000 15.000000 30 bd31 d Female 30.000000 16.000000 31 bd32 d Male 18.000000 11.000000 32 bd33 d Female 16.000000 10.000000 33 bd34 d Male 21.000000 11.000000 34 bd35 d Female 15.000000 10.000000 35 bd36 d Female 16.000000 10.000000 36 bd37 d Male 19.000000 14.000000 37 bd39 d Male 16.000000 10.000000 38 bd40 m Female 20.000000 14.000000 39 bd41 m Female 21.000000 15.000000 40 bd42 d Male 23.000000 9.000000 41 bd43 m Male 27.000000 9.000000 42 bd44 d Female 15.000000 8.000000 43 bd45 m Male 19.000000 9.000000 44 bd46 d Female 16.000000 11.000000 45 bd47 m Female 23.000000 15.000000 46 bd48 m Male 18.000000 13.000000 47 bd49 d Female 22.000000 15.000000 48 bd50 d Female 17.000000 11.000000 49 bd51 d Male 17.000000 10.000000 50 bd52 d Male 27.000000 15.000000 51 bd53 m Male 16.000000 9.000000 52 bd54 d Male 18.000000 12.000000 53 bd55 d Female 18.000000 11.000000 54 bd56 m Female 16.000000 10.000000 55 bd57 d Male 16.000000 9.000000 56 bd58 m Male 22.000000 9.000000 57 bd59 m Male 16.000000 8.000000 58 bd60 d Male 16.000000 9.000000 59 bd61 m Female 18.000000 10.000000 60 bd62 d Female 15.000000 9.000000 61 hc1 h Male 52.000000 7.000000 62 hc2 h Female 24.000000 10.000000 63 hc3 h Male 45.000000 7.000000 64 hc4 h Female 18.000000 13.000000 65 hc5 h Female 19.000000 10.000000 66 hc6 h Female 17.000000 12.000000 67 hc7 h Female 19.000000 7.000000 68 hc8 h Male 48.000000 5.000000 69 hc9 h Female 53.000000 6.000000 70 hc10 h Female 52.000000 15.000000 71 hc11 h Female 19.000000 12.000000 72 hc12 h Female 18.000000 12.000000 73 hc13 h Female 20.000000 12.000000 74 hc14 h Female 18.000000 12.000000 75 hc15 h Female 19.000000 13.000000 76 hc16 h Female 18.000000 11.000000 77 hc17 h Female 19.000000 12.000000 78 hc18 h Female 19.000000 12.000000 79 hc19 h Female 19.000000 12.000000 80 hc20 h Female 19.000000 12.000000 81 hc21 h Female 18.000000 12.000000 82 hc22 h Female 18.000000 12.000000 83 hc23 h Female 18.000000 11.000000 84 hc24 h Female 18.000000 12.000000 85 hc25 h Female 18.000000 12.000000 86 hc26 h Female 18.000000 11.000000 87 hc27 h Female 18.000000 12.000000 88 hc28 h Female 18.000000 12.000000 89 hc29 h Female 18.000000 11.000000 90 hc30 h Male 20.000000 12.000000 91 hc31 h Female 29.000000 17.000000 92 hc32 h Female 16.000000 10.000000 93 hc33 h Female 17.000000 10.000000 94 hc34 h Female 26.000000 14.000000 95 hc35 h Female 24.000000 17.000000 96 hc36 h Female 22.000000 17.000000 97 hc37 h Male 25.000000 17.000000 98 hc38 h Male 24.000000 17.000000 99 hc39 h Male 25.000000 17.000000 1 groups discrete 3 1 d 2 m 3 h 2 gender discrete 2 1 Male 2 Female 3 age continuous 0 4 edu continuous 0 Continuous Factors: Mean: StdDev: ------------------- ----- ------- age 22.293 9.015 edu 11.374 2.827 Number of subjects: 99 Number of factors: 4 (2 discrete, 2 continuous) Number of classes: 6 Number of regressors: 18 ============================================================ Data table loading completed successfully. SUBJECTS_DIR is '/media/root/Backup_Plus2/new/RECON' ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels ninputs = 99 Checking inputs nframestot = 99 Allocing output Done allocing nframes = 99 Writing to /media/root/Backup_Plus2/new/RECON/qdec/Untitled/y.mgh gdfRead(): reading /media/root/Backup_Plus2/new/RECON/qdec/Untitled/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 age 22.2929 8.96937 1 edu 11.3737 2.81262 Class Means of each Continuous Variable 1 groupsd-genderMale 19.0000 10.8000 2 groupsm-genderMale 24.1250 10.3750 3 groupsh-genderMale 34.1429 11.7143 4 groupsd-genderFemale 19.7647 11.9412 5 groupsm-genderFemale 24.8667 10.6000 6 groupsh-genderFemale 21.4375 11.9688 INFO: gd2mtx_method is dods Reading source surface /media/root/Backup_Plus2/new/RECON/fsaverage/surf/lh.white ERROR: no contrasts specified. Error in Analyze: command failed: mri_glmfit --y /media/root/Backup_Plus2/new/RECON/qdec/Untitled/y.mgh --fsgd /media/root/Backup_Plus2/new/RECON/qdec/Untitled/qdec.fsgd dods --glmdir /media/root/Backup_Plus2/new/RECON/qdec/Untitled --surf fsaverage lh --label /media/root/Backup_Plus2/new/RECON/fsaverage/label/lh.aparc.label —————————————————————————————————————————— I checked the description of .levels on the official website. I can use many categorical factors, but the error message is ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels https://secure-web.cisco.com/1kUfsJNAvGVt8tBXKDcJYuIUu4h1wAq2TNCeY2z4M_AAER… Can I use many categorical factors If I can, how can I solve this mistake

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Negative eTIV
by lqcheng2017 27 Mar '22

27 Mar '22

2 1

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