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 > wrote: > > On Sunday, April 20, 2014 2:25 AM, Bruce Fischl > 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 > > 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 > > > 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.
[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.
[Freesurfer] Fw: Fw: mri_watershed error, White Matter Intensity too high
On Sunday, April 20, 2014 2:25 AM, Bruce Fischl 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 > 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 > > 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] mri_watershed error, White Matter Intensity too high
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 : mri_watershed -atlas mprage_RPI.mgz mprage_skullstrip.mgz 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_preprocessings/HCV_subjects_2mm_Template/sub01/anat/mprage_skullstrip.mgz, -1): could not open file Error: input image mprage_orient not valid Thanks, Shahrzad___ 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: mri_watershed error, White Matter Intensity too high
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 > 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: mri_watershed error, White Matter Intensity too high
On Friday, April 18, 2014 11:43 PM, shahrzad kharabian 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.