[Freesurfer] Fw: mri_watershed error, White Matter Intensity too high
On Friday, April 18, 2014 11:43 PM, shahrzad kharabian shahrzad_k...@yahoo.com wrote: Dear experts, I have a encountered an Error while doing skull-stripping using freesurfer on my T1 weighted images, using mri_watershed I am using the following command: mri_watershed -atlas mprage_RPI.mgz mprage_skullstrip.mgz and here is the error: mri_watershed Error: w=White Matter =Intensity too high (240)...valid input ? I checked the images, actualy White matter intensity is around 300 . How could I overcome this issue? Bests, S.___ 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] Fw: Fw: mri_watershed error, White Matter Intensity too high
On Sunday, April 20, 2014 2:25 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Shahrzad can you cc the list so that others can answer? thanks Bruce On Sat, 19 Apr 2014, shahrzad kharabian wrote: Hi Bruce, True, I am trying to use Freesurfer skullstripping as a first step to create an input for Brain extraction tool of FSL so as to get in general acceptable extracted brains without changing BET options a lot for different brain. So, what I am doing is as following: I Deoblique anatomical image in AFNI. Then Bring it to FSL friendly orientation (RPI). Then, change the NIFTI format to mgz using mri_convert and then apply mdi_watershed using the command in the previous email. Here is the output of my anatomical scans preprocessing (including the watershed section) PREPROCESSING ANATOMICAL SCAN -- deobliquing sub01 anatomical ++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Apr 12 2012) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset mprage.nii.gz + loading and re-writing dataset mprage.nii.gz (./mprage.nii.gz+orig.HEAD in NIFTI storage) ++ 3drefit processed 1 datasets Reorienting sub01 anatomical skull stripping sub01 anatomical mri_convert --in_type nii --out_type mgz --input_volume mprage_RPI.nii --output_volume mprage_cut.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mprage_RPI.nii... 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 mprage_cut.mgz... Mode: Atlas analysis * The input file is mprage_cut.mgz The output file is mprage_skullstrip.mgz conforming input... MRIchangeType: Building histogram *WATERSHED** Sorting... first estimation of the COG coord: x=124 y=128 z=125 r=76 first estimation of the main basin volume: 1892714 voxels mri_watershed Error: w=White Matter =Intensity too high (240)...valid input ? mri_convert -i mprage_skullstrip.mgz -o mprage_orient.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mprage_skullstrip.mgz... mghRead(/scr/somalia3/HEP_C_total_II/restingstate_analysis/fconscript_prepr ocessings/HCV_subjects_2mm_Template/sub01/anat/mprage_skullstrip.mgz, -1): could not open file Error: input image mprage_orient not valid Thanks, Shahrzad On Saturday, April 19, 2014 3:43 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: can you send us the entire output of the command? And perhaps some background? I assume you are trying to use mri_watershed outside of recon-all? On Sat, 19 Apr 2014, shahrzad kharabian wrote: On Friday, April 18, 2014 11:43 PM, shahrzad kharabian shahrzad_k...@yahoo.com wrote: Dear experts, I have a encountered an Error while doing skull-stripping using freesurfer on my T1 weighted images, using mri_watershed I am using the following command: mri_watershed -atlas mprage_RPI.mgz mprage_skullstrip.mgz and here is the error: mri_watershed Error: w=White Matter =Intensity too high (240)...valid input ? I checked the images, actualy White matter intensity is around 300 . How could I overcome this issue? Bests, S. 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 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] rmanova contrast file error
Dear Experts, I am running a rmanova using FSGD file and mri_glmfit. I have done the mris_preproc step, and am currently trying to do the mri_glmfit step. I keep getting an error that appears to be related to the contrast files and matricies (highlighted in yellow below) I have also attched the FSGD file and a contrast file. Everything is in ASCII. The output from the command terminal is below: mri_glmfit --glmdir lh.rmanova --y lh.thickness.mgh --fsgd rmanova.fsgd doss --C tp1_vs_tp2.mtx --C tp1_vs_tp3.mtx --C tp2_vs_tp3.mtx --C tp_effect.mtx --C mean.mtx --surface fsaverage lh gdfReadHeader: reading rmanova.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 tp1_vs_tp2 0 0.840168 1 tp2_vs_tp3 0 0.766965 Class Means of each Continuous Variable 1 ECT_001 0. 0. 2 ECT_002 0. 0. 3 ECT_003 0. 0. 4 ECT_004 0. 0. 5 ECT_005 0. 0. 6 ECT_006 0. 0. 7 ECT_007 0. 0. 8 ECT_008 0. 0. 9 ECT_009 0. 0. 10 ECT_010 0. 0. 11 ECT_011 0. 0. 12 ECT_012 0. 0. 13 ECT_013 0. 0. 14 ECT_014 0. 0. 15 ECT_015 0. 0. 16 ECT_016 0. 0. 17 ECT_017 0. 0. 18 ECT_018 0. 0. 19 ECT_019 0. 0. 20 ECT_020 0. 0. 21 ECT_021 0. 0. 22 ECT_022 0. 0. 23 ECT_023 0. 0. 24 ECT_024 0. 0. INFO: gd2mtx_method is doss Reading source surface /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1/fsaverage/surf/lh.white Number of vertices 163842 Number of faces327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1 cmdline mri_glmfit --glmdir lh.rmanova --y lh.thickness.mgh --fsgd rmanova.fsgd doss --C tp1_vs_tp2.mtx --C tp1_vs_tp3.mtx --C tp2_vs_tp3.mtx --C tp_effect.mtx --C mean.mtx --surface fsaverage lh sysname Linux hostname fs-OptiPlex-755 machine i686 user fs FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1/lh.thickness.mgh logyflag 0 usedti 0 FSGD rmanova.fsgd labelmask /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.rmanova IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.rmanova Loading y from /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1/lh.thickness.mgh INFO: gd2mtx_method is doss Saving design matrix to lh.rmanova/Xg.dat Normalized matrix condition is 2.67942 Matrix condition is 32.198 Found 149955 points in label. Pruning voxels by thr: 0.00 Found 148274 voxels in mask Saving mask to lh.rmanova/mask.mgh Reshaping mriglm-mask... search space = 73670.427324 MatrixReadTxT: could not scan value [2][1] ERROR: loading C tp1_vs_tp2.mtx Any help would be greatly appreciated. Thanks, Harry Harry Hallock | MPhil Candidate Regenerative Neuroscience Group | Brain Mind Research Institute THE UNIVERSITY OF SYDNEY Room 408, Level 4, M02K | 94 Mallett St Camperdown | NSW | 2050 | Australia T +61 2 9114 4138 F +61 9351 0930 E hhal5...@uni.sydney.edu.au | W www.rng.org.au rmanova.fsgd Description: rmanova.fsgd tp1_vs_tp2.mtx Description: tp1_vs_tp2.mtx ___ 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] Fw: Fw: mri_watershed error, White Matter Intensity too high
Try running mri_normalize first Cheers Bruce On Apr 19, 2014, at 9:21 PM, shahrzad kharabian shahrzad_k...@yahoo.com wrote: On Sunday, April 20, 2014 2:25 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Shahrzad can you cc the list so that others can answer? thanks Bruce On Sat, 19 Apr 2014, shahrzad kharabian wrote: Hi Bruce, True, I am trying to use Freesurfer skullstripping as a first step to create an input for Brain extraction tool of FSL so as to get in general acceptable extracted brains without changing BET options a lot for different brain. So, what I am doing is as following: I Deoblique anatomical image in AFNI. Then Bring it to FSL friendly orientation (RPI). Then, change the NIFTI format to mgz using mri_convert and then apply mdi_watershed using the command in the previous email. Here is the output of my anatomical scans preprocessing (including the watershed section) PREPROCESSING ANATOMICAL SCAN -- deobliquing sub01 anatomical ++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Apr 12 2012) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset mprage.nii.gz + loading and re-writing dataset mprage.nii.gz (./mprage.nii.gz+orig.HEAD in NIFTI storage) ++ 3drefit processed 1 datasets Reorienting sub01 anatomical skull stripping sub01 anatomical mri_convert --in_type nii --out_type mgz --input_volume mprage_RPI.nii --output_volume mprage_cut.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mprage_RPI.nii... 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 mprage_cut.mgz... Mode: Atlas analysis * The input file is mprage_cut.mgz The output file is mprage_skullstrip.mgz conforming input... MRIchangeType: Building histogram *WATERSHED** Sorting... first estimation of the COG coord: x=124 y=128 z=125 r=76 first estimation of the main basin volume: 1892714 voxels mri_watershed Error: w=White Matter =Intensity too high (240)...valid input ? mri_convert -i mprage_skullstrip.mgz -o mprage_orient.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mprage_skullstrip.mgz... mghRead(/scr/somalia3/HEP_C_total_II/restingstate_analysis/fconscript_prepr ocessings/HCV_subjects_2mm_Template/sub01/anat/mprage_skullstrip.mgz, -1): could not open file Error: input image mprage_orient not valid Thanks, Shahrzad On Saturday, April 19, 2014 3:43 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: can you send us the entire output of the command? And perhaps some background? I assume you are trying to use mri_watershed outside of recon-all? On Sat, 19 Apr 2014, shahrzad kharabian wrote: On Friday, April 18, 2014 11:43 PM, shahrzad kharabian shahrzad_k...@yahoo.com wrote: Dear experts, I have a encountered an Error while doing skull-stripping using freesurfer on my T1 weighted images, using mri_watershed I am using the following command: mri_watershed -atlas mprage_RPI.mgz mprage_skullstrip.mgz and here is the error: mri_watershed Error: w=White Matter =Intensity too high (240)...valid input ? I checked the images, actualy White matter intensity is around 300 . How could I overcome this issue? Bests, S. 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
