Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30133 discussions

Re: [Freesurfer] mri_glmfit help
by Douglas N Greve 16 Jan '14

16 Jan '14

you have to use your own regressor. This is not usually done with thickness because thickness does not scale with head size On 01/16/2014 04:32 PM, Danielle Miller wrote: > Hi Doug, > > Thank-you for the responses! > > An additional question: does mri_glmfit or preproc take into account > head size? Or will I need to correct for that on my own by including > it as a regressor? > > Thanks, > Danielle > > -- > Ph.D. Program in Behavioral Neuroscience > Boston University School of Medicine L-815 > 72 E. Concord St > Boston, MA 02118 > > > VA Boston Healthcare System Jamaica Plain > Memory Disorders Research Center > 150 South Huntington Ave D11-103 > Boston, MA 02130 > OFFICE:(857) 364-2130 > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

mri_glmfit help
by Danielle Miller 16 Jan '14

16 Jan '14

Hi Freesurfer Experts, I have some questions regarding mri_glmfit - some basic and some not so basic - that I hope you can help me with. 1.) I want to do a thickness analysis looking at the effect of a continuous variable on thickness while regressing out effects of both continuous and categorical variables. Let's just say I have one continuous variable of interest, one to regress out, and one categorical variable (with four groups) to regress out. From reading other posts, it seems that I should make my categorical variables into a class - if I do this will this contrast look at the effect of my continuous variable while regressing out effects from the other variables (including group)? This is assuming I am running a DOSS analysis 0 0 0 0 0 1 2.) In the cluster corrected significant image, I am a bit confused on what the positive and negative significance values represent. If I was looking at group differences - would red indicate that the first group > second group, and blue indicate first group < second group (that is, first group with increased or decreased thickness compared to second group)? 3.) Lastly, I see that you can use mris_preproc and glmfit to look at volume. Does this look at volume in a voxel-based way? That is, is it comparing volume on a voxel level? If so, would the correct commands be: mris_preproc --fsgd FSGD FILE --target fsaverage --hemi lh --meas volume --out OUT.mgh mri_glmfit --y MGH FILE --fsgd FSGD FILE doss --C CONTRAST --surf fsaverage lh --glmdir GLM DIR Would I need to smooth the data? Thanks for any and all help! Danielle -- Ph.D. Program in Behavioral Neuroscience Boston University School of Medicine L-815 72 E. Concord St Boston, MA 02118 VA Boston Healthcare System Jamaica Plain Memory Disorders Research Center 150 South Huntington Ave D11-103 Boston, MA 02130 OFFICE:(857) 364-2130

2 1

data qcached in different FS versions
by Alexander Lebedev 16 Jan '14

16 Jan '14

*Dear Freesurfers,* I have quite a large dataset processed with FS 5.1. However, half of the output was qcached in FS 5.3. I just wanted to clarify whether I should rerun qcache in FS 5.1 for the whole set. If not, could you please confirm that this command does the same across different versions (REF: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19370.html)? Of note, I am going to use unsmoothed output. *===* *Best Regards,* *Alexander Lebedev* Stavanger University Hospital, Norway

2 1

Applying mask with mri_mask
by Arash Jalalian 16 Jan '14

16 Jan '14

Hi, I would like to apply white matter mask (wm.mgz) produced by freesurfer recon-all command on FLAIR. The FLAIR and wm.mgz have different dimensions such that Flair is 512by512 while wm.mgz has 256by256 in dimensions. I tried to fix this by resizing the flair in matlab but after applying the mask the result is not good. I don't get the difference in dimension anymore though. Is there any way that I can resize a mgz volume in freesurfer? Many thanks, Arash

2 1

Folder organization cross-sectional/longitudinal analysis
by Janosch Linkersdörfer 16 Jan '14

16 Jan '14

Hi all, I have 4 years of structural scans from children and 2 from adults. I would like to analyze the data both cross-sectionally and longitudinally. In the recommendations for the longitudinal analysis, it says one should process all images in one folder with the time point in the subjectID/subject folder, e.g., .../data/tp1_subj001 .../data/tp2_subj001 .../data/tp3_subj001 .../data/tp4_subj001 .../data/tp1_subj002 ... For the cross-sectional analyses, I would like to organize the analyses in folders for subject age and year, e.g., .../data/children/tp1/subj001 .../data/children/tp1/subj002 .../data/children/tp2/subj001 .../data/children/tp2/subj002 ... .../data/adults/tp1/adult_subj001 .../data/adults/tp1/adult_subj002 .../data/adults/tp2/adult_subj001 .../data/adults/tp2/adult_subj001 Is it possible to organize the data this way and to symlink the individual folders into another folder for the longitudinal analysis, i.e., .../longitudinal_analysis/tp1_subj001 -> .../data/children/tp1/subj001 .../longitudinal_analysis/tp2_subj001 -> .../data/children/tp2/subj001 ... Additionally, are there any considerations regarding renaming/moving subject folders (as long as anything inside a subject folder remains unchanged), i.e. are there any hard links or similar that would break further processing? Thanks a lot! Janosch

3 6

Applying mask with mdi_mask
by Arash Jalalian 15 Jan '14

15 Jan '14

1 0

Saving bbregister result as a volume
by Arash Jalalian 15 Jan '14

15 Jan '14

Hi free surfer community, I am trying to register Flair with T1 using bbregister and save the result as a volume so I can open it in my application that I am developing. I managed to obtain the register.dat and also to see the result using tkregister2. I was wondering if I can apply the transform provided in register.dat on a volume and save the output as mgz file. Thanks, Arash

2 1

mri_vol2surf - best way to avoid partial voluming?
by Josef Ling 15 Jan '14

15 Jan '14

I'd like to project functional data onto the surface for group analysis. I'd like to limit partial voluming when selecting values with mri_vol2surf. I noticed that the default projfrac = 0 for mri_vol2surf which seems to me it would select a number of values contaminated by WM. Why is the default = 0? >From the examples below, which is the soundest method of selecting representative GM only values? Please correct any errors in my understanding. :) mri_vol2surf --projfrac 0.5 --interp nearest --surf white This would select a single value closest to halfway up the normal vector from the WM vertex. mri_vol2surf --projfrac 0.5 --interp trilin --surf white This would interpolate from multiple nearby values halfway up the normal vector from the WM vertex. mri_vol2surf --projfrac-avg 0.25 0.75 0.25 --surf white Average from two values a quarter of the way up and down? Thanks

2 1

(no subject)
by Hugh Pemberton 15 Jan '14

15 Jan '14

hi guys i'm getting a 'Couldn't create output file .xdebug_tkmedit' before loading volumes, any suggestions on what I can do would be most welcome. Also got: ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu : : Now exiting... : When taking a volume snapshot and then freesurfer shut down but there's no file for me to send you, I've just installed on a mac lion v5.3.0 Cheers! Hugh

2 1

dt_recon b-values and b-vectors
by Swartz, Max 14 Jan '14

14 Jan '14

Howdy, I'm trying to run *dt_recon* on some DTI data but seem to be having some trouble with the number of b-values and b-vectors not matching the number of data frames we have (see dt_recon logfile below). Some basic parameters of our sequence are as follows: - TR = 10 s - TE = 96.2 ms - slice thickness = 4 mm - FOV = 25.6 cm 9 25.6 cm - flip angle = 90 - slice orientation= axial - matrix size = 64 x 64 - maximum b value = 1,000.65 The scan was developed from the protocol described in the following paper: http://link.springer.com/content/pdf/10.1007%2Fs00429-013-0506-x.pdf The scan is supposed to be in 30 directions, but we have 36 b-values and b-vectors. Our DTI EPI BRIK file contains 28 data frames. It is my understanding that these three values should match, but I am lost when it comes to execution of this task. Our b-values, b-vectors, and dt_recon.log file are shown below: *bval:* 0 999.4792194 999.2313486 1000.074909 998.9414996 999.2023637 1000.18885 0 999.3712757 998.6526501 999.0604376 998.6166688 1000.30379 998.9614892 0 998.9295058 998.802572 999.6841127 999.3692767 1000.26581 998.9774808 0 999.8200418 1000.64961 1000.268808 999.6821137 999.595159 999.5162001 0 999.8890059 999.7680689 999.378272 999.6581262 999.645133 998.8895267 0 *bvec:* 0 0 0 1 0 0 0.166 0.986 0 -0.11 0.664 0.74 0.901 -0.419 -0.11 -0.169 -0.601 0.781 -0.815 -0.386 0.433 0 0 0 0.656 0.366 0.66 0.582 0.8 0.143 0.9 0.259 0.35 0.693 -0.698 0.178 0.357 -0.924 -0.14 0.543 -0.488 -0.683 0 0 0 -0.525 -0.396 0.753 -0.639 0.689 0.341 -0.33 -0.013 -0.944 -0.524 -0.783 0.335 0.609 -0.065 -0.791 0.22 -0.233 -0.947 0 0 0 -0.004 -0.91 -0.415 -0.511 0.627 -0.589 0.414 0.737 0.535 -0.679 0.139 -0.721 0.884 -0.296 0.362 0.262 0.432 0.863 0 0 0 0.088 0.185 -0.979 0.294 -0.907 0.302 0.887 -0.089 -0.453 0.257 -0.443 0.859 0.086 0.867 -0.491 0.863 0.504 -0.025 0 0 0 dt_recon logfile Tue Jan 14 11:03:29 EST 2014 VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $ setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /data/swartzms/dbdr/dbdr_analysis/cals_football/data_files /usr/local/freesurfer/bin/dt_recon --i /usr/local/freesurfer/subjects/802_ucni_FS/mri/orig/802_DTI+orig.BRIK --s 802_ucni_FS --o /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files --b /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bval /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bvec xoth2 swartzms /usr/share/fsl/5.0/bin/eddy_correct ECRefTP 0 #@#------------------------------- Converting input Tue Jan 14 11:03:29 EST 2014 cd /data/swartzms/dbdr/dbdr_analysis/cals_football/data_files mri_convert /usr/local/freesurfer/subjects/802_ucni_FS/mri/orig/802_DTI+orig.BRIK /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi.nii mri_convert /usr/local/freesurfer/subjects/802_ucni_FS/mri/orig/802_DTI+orig.BRIK /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi.nii warning: string DATASET_NAME does not end with "~" $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/802_ucni_FS/mri/orig/802_DTI+orig.BRIK... AFNI Header Information ============================================ DATASET_RANK : spatial dims 3, sub-bricks 28 DATASET_DIMENSIONS: (64, 64, 35) TYPESTRING : 3DIM_HEAD_ANAT SCENE_DATA : view type 0, func type 2, verify 0 ORIGIN : (126.000000, -126.000000, -68.000000) DELTA : (-4.000000, 4.000000, 4.000000) IDCODE_STRING : CIR_2tEY1lHce4a BYTEORDER_STRING : LSB_FIRST BRICK_STATS : min 0.000000 max 128.024994 BRICK_STATS : min 0.000000 max 21.291500 BRICK_STATS : min 0.000000 max 29.162399 BRICK_STATS : min 0.000000 max 20.906200 BRICK_STATS : min 0.000000 max 20.719999 BRICK_STATS : min 0.000000 max 22.354900 BRICK_STATS : min 0.000000 max 21.723499 BRICK_STATS : min 0.000000 max 126.376999 BRICK_STATS : min 0.000000 max 21.332399 BRICK_STATS : min 0.000000 max 23.682100 BRICK_STATS : min 0.000000 max 20.807301 BRICK_STATS : min 0.000000 max 23.097000 BRICK_STATS : min 0.000000 max 23.482201 BRICK_STATS : min 0.000000 max 23.115200 BRICK_STATS : min 0.000000 max 119.787003 BRICK_STATS : min 0.000000 max 23.863899 BRICK_STATS : min 0.000000 max 22.267799 BRICK_STATS : min 0.000000 max 21.466900 BRICK_STATS : min 0.000000 max 22.947701 BRICK_STATS : min 0.000000 max 20.433399 BRICK_STATS : min 0.000000 max 20.641600 BRICK_STATS : min 0.000000 max 127.492996 BRICK_STATS : min 0.000000 max 22.346399 BRICK_STATS : min 0.000000 max 20.726400 BRICK_STATS : min 0.000000 max 21.634701 BRICK_STATS : min 0.000000 max 19.920799 BRICK_STATS : min 0.000000 max 20.998699 BRICK_STATS : min 0.000000 max 21.381701 BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_TYPES : complex BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 BRICK_FLOAT_FACS : 0.000000 ==================================================================== INFO: number of frames dataset_rank[1] = 28 : numtypes = 28 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 128.024994 <--> actual max = 128.024704 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 21.291500 <--> actual max = 21.291540 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 29.162399 <--> actual max = 29.162401 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.906200 <--> actual max = 20.906200 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.719999 <--> actual max = 20.720045 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 22.354900 <--> actual max = 22.354910 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 21.723499 <--> actual max = 21.723537 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 126.376999 <--> actual max = 126.377357 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 21.332399 <--> actual max = 21.332430 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 23.682100 <--> actual max = 23.682091 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.807301 <--> actual max = 20.807331 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 23.097000 <--> actual max = 23.096958 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 23.482201 <--> actual max = 23.482182 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 23.115200 <--> actual max = 23.115194 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 119.787003 <--> actual max = 119.786865 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 23.863899 <--> actual max = 23.863934 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 22.267799 <--> actual max = 22.267784 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 21.466900 <--> actual max = 21.466867 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 22.947701 <--> actual max = 22.947695 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.433399 <--> actual max = 20.433388 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.641600 <--> actual max = 20.641575 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 127.492996 <--> actual max = 127.493370 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 22.346399 <--> actual max = 22.346439 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.726400 <--> actual max = 20.726437 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 21.634701 <--> actual max = 21.634733 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 19.920799 <--> actual max = 19.920761 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 20.998699 <--> actual max = 20.998676 BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 21.381701 <--> actual max = 21.381670 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) writing to /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi.nii... #@#------------------------------- Eddy/Motion Correct Tue Jan 14 11:03:30 EST 2014 cd /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/ectmp eddy_correct /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi.nii /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec.nii 0 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0000 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0001 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0002 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0003 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0004 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0005 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0006 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0007 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0008 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0009 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0010 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0011 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0012 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0013 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0014 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0015 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0016 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0017 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0018 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0019 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0020 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0021 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0022 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0023 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0024 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0025 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0026 processing /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec_tmp0027 #@#------------------------------- Fitting Tensors Tue Jan 14 11:10:32 EST 2014 cd /data/swartzms/dbdr/dbdr_analysis/cals_football/data_files mri_glmfit --y /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec.nii --glmdir /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files --dti /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bval /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bvec $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /data/swartzms/dbdr/dbdr_analysis/cals_football/data_files cmdline mri_glmfit --y /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec.nii --glmdir /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files --dti /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bval /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bvec sysname Linux hostname xoth2 machine x86_64 user swartzms FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec.nii logyflag 1 usedti 1 glmdir /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files Loading y from /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/dwi-ec.nii Using DTI Loading BValues from /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bval Found 36 bvalues Loading BVectors from /data/swartzms/dbdr/dbdr_analysis/cals_football/SCRIPTS/UCNI.bvec Found 36 bvectorss Detected BVec file as MGH formatted Saving design matrix to /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/Xg.dat Normalized matrix condition is 23.5551 Matrix condition is 1.66263e+06 Pruning voxels by thr: 50.000000 Found 255 voxels in mask Saving mask to /usr/local/freesurfer/subjects/802_ucni_FS/DTI_files/mask.nii search space = 16320.000000 ERROR: dimension mismatch between y and X. y has 28 inputs, X has 36 rows. Any suggestions or insight you can provide is much appreciated. Thanks in advance, - Max -- Max Swartz Biochemistry and Biological Physics Miami University | Oxford, OH 513.886.6574

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer