hi, Bronwyn
You should change the position of parameter "dods" like this:
mri_glmfit --fsgd long-2stage_ConAR.fsgd dods --glmdir long-2stage_ConAR.area.lh.spc.glmdir --y long-ConAR.lh.area-spc.stack.fwhm10.mgh
Hope this helps.
Best, Feng
发件人：Bronwyn Overs b.overs@neura.edu.au 发送时间：2015-10-14 08:11 主题：[Freesurfer] Problem with fsgd file 收件人："Freesurfer support list"freesurfer@nmr.mgh.harvard.edu 抄送：
Dear mailing list,
I am trying to run a longitudinal 2 stage model using mri_glmfit. Here is the command I am using:
mri_glmfit --fsgd long-2stage_ConAR.fsgd --glmdir long-2stage_ConAR.area.lh.spc.glmdir --y long-ConAR.lh.area-spc.stack.fwhm10.mgh dods --C me_age-all.mtx --C me_gender.mtx --C me_group.mtx --C int_ageXgroup.mtx --C int_ageXgender.mtx --C int_genderXgroup.mtx --C int_ageXgenderXgroup.mtx --surf fsaverage lh --label long-ConAR.lh.area.fsaverage.cortex.label
However, when I try to run the command it has problems reading my fsgd file. I have attached my file for reference and here are the errors it spits out:
gdfReadHeader: reading long-2stage_ConAR.fsgd INFO: ignoring tag 7541001001 INFO: ignoring tag 7541002001 INFO: ignoring tag 7541003001 INFO: ignoring tag 7541006001 INFO: ignoring tag 7541009001 INFO: ignoring tag 7541011004 INFO: ignoring tag 7541012004 INFO: ignoring tag 7541017001 INFO: ignoring tag 7541018001 INFO: ignoring tag 7541020001 INFO: ignoring tag 7541022001 INFO: ignoring tag 7541023001 INFO: ignoring tag 7541024001 INFO: ignoring tag 7541026001 INFO: ignoring tag 7541030001 INFO: ignoring tag 7541031001 INFO: ignoring tag 7541036001 INFO: ignoring tag 7541040001 INFO: ignoring tag 7541041001 INFO: ignoring tag 7541042001 INFO: ignoring tag 7541044001 INFO: ignoring tag 7541046001 INFO: ignoring tag 7541047001 INFO: ignoring tag 7541048004 INFO: ignoring tag 7541049001 INFO: ignoring tag 7541052001 INFO: ignoring tag 7541055001 INFO: ignoring tag 7541057001 INFO: ignoring tag 7541058001 INFO: ignoring tag 7541059001 INFO: ignoring tag 7541060001 INFO: ignoring tag 7541062001 INFO: ignoring tag 7541070001 INFO: ignoring tag 7541075001 INFO: ignoring tag 7541078001 INFO: ignoring tag 7541080001 INFO: ignoring tag 7541084001 INFO: ignoring tag 7541085001 INFO: ignoring tag 7541088001 INFO: ignoring tag 7541090001 INFO: ignoring tag 7541093001 INFO: ignoring tag 7541094001 INFO: ignoring tag 7541096001 INFO: ignoring tag 7541097004 INFO: ignoring tag 7541099001 INFO: ignoring tag 7541100001 INFO: ignoring tag 7541101001 INFO: ignoring tag 7541102001 INFO: ignoring tag 7541103001 INFO: ignoring tag 7541106001 INFO: ignoring tag 7541108001 INFO: ignoring tag 7541110004 INFO: ignoring tag 7541112001 INFO: ignoring tag 7541114001 INFO: ignoring tag 7541116001 INFO: ignoring tag 7541118001 INFO: ignoring tag 7541119001 INFO: ignoring tag 7541120001 INFO: ignoring tag 7541124001 INFO: ignoring tag 7541125001 INFO: ignoring tag 7541132004 INFO: ignoring tag 7541133001 INFO: ignoring tag 7541139001 INFO: ignoring tag 7541142001 INFO: ignoring tag 7541143001 INFO: ignoring tag 7541146001 INFO: ignoring tag 7541149001 INFO: ignoring tag 7541150001 INFO: ignoring tag 7541151001 INFO: ignoring tag 7541156001 INFO: ignoring tag 7541161001 INFO: ignoring tag 7541165001 INFO: ignoring tag 7541168001 INFO: ignoring tag 7541175001 INFO: ignoring tag 7541177001 INFO: ignoring tag 7541178001 INFO: ignoring tag 7541182001 INFO: ignoring tag 7541185001 INFO: ignoring tag 7541188001 INFO: ignoring tag 7541190004 INFO: ignoring tag 7541192004 INFO: ignoring tag 7541196001 INFO: ignoring tag 7541198001 INFO: ignoring tag 7541209001 INFO: ignoring tag 7541223001 INFO: ignoring tag 7541227001 INFO: ignoring tag 7541334001 INFO: ignoring tag 7541337001 INFO: ignoring tag 7541345001 INFO: ignoring tag 7541346001 INFO: ignoring tag 7541353001 INFO: ignoring tag 7541366001 INFO: ignoring tag 7541378001 INFO: ignoring tag 7541383001 INFO: ignoring tag 7541388001 INFO: ignoring tag 7541391001 INFO: ignoring tag 7541396001 INFO: ignoring tag 7541400001 INFO: ignoring tag 7541401001 INFO: ignoring tag 7541402001 INFO: ignoring tag 7541409001 INFO: ignoring tag 7541411001 INFO: ignoring tag 7541412001 INFO: ignoring tag 7541421001 INFO: ignoring tag 7541442004 INFO: ignoring tag 7541443001 INFO: ignoring tag 7541445001 WARNING: gdfReadV1: class genderM-groupCtl is defined but not used. INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 years -nan -nan 1 age_mc -nan -nan Class Means of each Continuous Variable 1 genderM-groupCtl -nan -nan 2 genderF-groupCtl -nan -nan 3 genderM-groupAR -nan -nan 4 genderF-groupAR -nan -nan INFO: gd2mtx_method is dods ERROR: Option dods unknown
Can you tell me what is wrong?
Kind regards, Bronwyn Overs Research Assistant
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 neura.edu.au
