Freesurfer

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30099 discussions

rmanova contrast file error
by Harry Hallock [hhal5293＠uni.sydney.edu.au] 22 Apr '14

22 Apr '14

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 0.0000 0.0000 2 ECT_002 0.0000 0.0000 3 ECT_003 0.0000 0.0000 4 ECT_004 0.0000 0.0000 5 ECT_005 0.0000 0.0000 6 ECT_006 0.0000 0.0000 7 ECT_007 0.0000 0.0000 8 ECT_008 0.0000 0.0000 9 ECT_009 0.0000 0.0000 10 ECT_010 0.0000 0.0000 11 ECT_011 0.0000 0.0000 12 ECT_012 0.0000 0.0000 13 ECT_013 0.0000 0.0000 14 ECT_014 0.0000 0.0000 15 ECT_015 0.0000 0.0000 16 ECT_016 0.0000 0.0000 17 ECT_017 0.0000 0.0000 18 ECT_018 0.0000 0.0000 19 ECT_019 0.0000 0.0000 20 ECT_020 0.0000 0.0000 21 ECT_021 0.0000 0.0000 22 ECT_022 0.0000 0.0000 23 ECT_023 0.0000 0.0000 24 ECT_024 0.0000 0.0000 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 faces 327680 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: 0.000000 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 hhal5293(a)uni.sydney.edu.au | W www.rng.org.au

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resetting wm-mean [CA Normalize]
by Mark Plantz 21 Apr '14

21 Apr '14

Hi freesurfers, I am running into an error where the white matter and gray matter means of my atlas are automatically setting to 0 during the #@# CA Normalize pathway. I copied a code segment below to help explain better. Has anyone else run into this problem? Is there a way to manually change these averages? *#@# CA Normalize Mon Apr 14 17:03:07 CDT 2014* */Applications/freesurfer/subjects/CMH-11780/mri* *\n mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /Applications/freesurfer/average/atlas2.gca transforms/talairach.lta norm.mgz \n* *writing control point volume to ctrl_pts.mgz* *using MR volume brainmask.mgz to mask input volume...* *reading 1 input volume* *reading atlas from '/Applications/freesurfer/average/atlas2.gca'...* *reading transform from 'transforms/talairach.lta'...* *reading input volume from nu.mgz...* *resetting wm mean[0]: 0 --> 0* *resetting gm mean[0]: 0 --> 0* *input volume #1 is the most T1-like* *using real data threshold=27.0* *skull bounding box = (64, 79, 51) --> (194, 166, 204)* *using (107, 108, 128) as brain centroid...* *mean wm in atlas = 0, using box (91,97,109) --> (122, 118,146) to find MRI wm* *before smoothing, mri peak at 110* *after smoothing, mri peak at 111, scaling input intensities by 0.000* *scaling channel 0 by 0* *using 136509 sample points...* *INFO: compute sample coordinates transform* * 1.000 0.000 0.000 0.000;* * 0.000 1.000 0.000 0.000;* * 0.000 0.000 1.000 0.000;* * 0.000 0.000 0.000 1.000;* *INFO: transform used* Thank you for the help. - MP

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An overwrite issue with selxavg3-sess
by Reza Rajimehr 21 Apr '14

21 Apr '14

I have done a functional analysis for some contrasts using selxavg3-sess. In the contrast folders, I have added some files. Now I want to do the same analysis for some new contrasts. My guess is that selxavg3-sess computes all the contrasts again, and I am worried that the new folders overwrite the previous ones and I lose the files that I have manually added. If this is the case, is there a way to run selxavg3-sess for some specified contrasts? Thanks, Reza

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Fw: Fw: mri_watershed error, White Matter Intensity too high
by shahrzad kharabian 20 Apr '14

20 Apr '14

On Sunday, April 20, 2014 2:25 AM, Bruce Fischl <fischl(a)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 > <fischl(a)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_kh_m(a)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. > > > > >

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mri_watershed error, White Matter Intensity too high
by shahrzad kharabian 19 Apr '14

19 Apr '14

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

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mri_watershed error, White Matter Intensity too high
by shahrzad kharabian 19 Apr '14

19 Apr '14

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.

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Research Coordinator Job: Northwestern Univ. Alzheimer's Disease Center (Chicago, IL)
by Emily Rogalski 18 Apr '14

18 Apr '14

Research Coordinator job available at Northwestern University’s Cognitive Neurology and Alzheimer’s Disease Center in Chicago, IL. The research assistant will be responsible for analysis of neuroimaging datasets, in order to contribute to neuroscientific studies of normal aging and pathological aging. Duties include coordinating PET and MRI scans, and analyzing the resultant structural and functional imaging data. Additional duties include working on graphics for manuscripts and grants or other general lab responsibilities. Candidates must have proficiency with computer programming, ideally with relevant technical languages such as MATLAB or Python. They must be willing to learn new MRI analysis software and troubleshoot problems independently. Prior experience with neuroimaging analysis suites such as Freesurfer, FSL, or SPM would be extremely useful. Relevant backgrounds would be in Neuroscience, Biology, Psychology, Computer Science, Mathematics, and Biomedical Engineering. *Minimum Qualifications: * - The candidate must hold a Bachelor degree. - Candidate must be fluent in at least one programming language. - A two-year commitment is requested. *Preferred Qualifications: * - Experience using Freesurfer or other neuroimaging platforms. Interested applicants can apply online here: http://www.northwestern.edu/hr/careers/ Job ID: 23069 If you have specific questions please email: e-rogalski(a)northwestern.edu To learn more about our center please go to: www.brain.northwestern.edu -- Emily J Rogalski, PhD Associate Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogalski(a)gmail.com

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RAS to MNI coordinate conversion function?
by John Pyles 18 Apr '14

18 Apr '14

Hi, I am not a heavy Freesurfer user and I haven't had good luck figuring this out through the FreeSurfer documentation and I thought an expert might have a fast answer. If anyone has an easy solution it would be very much appreciated. While I use FreeSurfer for automatic segmentation, I don't normally use if for analysis. However for an ECoG project I'm using parts of FreeSurfer to aid in electrode coregistration. Basically the issue is that I have electrode coordinates in what I believe are FreeSurfer RAS space and I need to convert them to MNI space. I have many of these electrode coordinates for each subject so I need a FreeSurfer or Matlab function to automate this process. Is there a simple way to do this? The *very* kludgy way I figured out how to do this "manually" is as follows (I'm sure this is going to seem very dumb to a FreeSurfer user, but I needed a quick solution that worked for a figure). 1) Enter the coordinate output from my electrode coregistration routines manually into the RAS field in Freeview. 2) Take the "brain volume" coordinates (all positive) in Freeview and enter them into the "Volume Coordinate" field in TkMedit. 3) Copy the TAL coordinates output in MkEdit when the brain volume coordinate is entered. 4) Convert the TAL coordinates to MNI in Matlab with tal2mni.m It seems like there should be a simple function to do this coordinate conversion using the transformation info from recon-all that I'm assuming both Freeview and TkMedit use, but I can't seem to find it? Any help would be appreciated. Thanks again! Best, John ______________________________________ John Pyles, Ph.D. Research Scientist Center for the Neural Basis of Cognition Department of Psychology Carnegie Mellon University ______________________________________

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convert tlrc mask into surface
by charujing123 18 Apr '14

18 Apr '14

Hi FS experts, I have a ROI mask in tlrc coordinates in *.tlrc file format, which represents functional activation. Also I have a significant area in sig.mgh which represents cortical thickness difference between two groups, and I created a mask based on surface for it. Now I want to compare these two masks and detect whether there is any overlapped area in them. Thanks All the best. Rujing Zha 2014-04-18 charujing123

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quality T1 for new study
by Kok, JG (neuro) 18 Apr '14

18 Apr '14

Dear Freesurfer experts, I uploaded a .nii.gz file (which can be downloaded from 'http://gate.nmr.mgh.harvard.edu/filedrop2/?p=7pbsgklemux'). I hope you would be willing to comment on the quality of this scan for use with Freesurfer (you can find some parameters below; the scan was acquired on a 3T Philips scanner). Running it through recon-all seems to give nice results, but then again, I am in a phase of running pilots before the start of a new study, and I do not have much experience with Freesurfer results yet. coil: 32 channel Sequence: T1w_TFE_3D TFE factor: 256 Acquisition time: 10:14 FoV FH256xAP256xRL160 mm 160 sagittal slices fold-over direction AP fat shift direction F scan mode 3D acquisition matrix 256 x 256 acquisition voxel size 1.00/1.00/1.00 reconstructed voxel size 1.00/1.00/1.00 TR shortest (=7.6ms) TE shortest (=3.5ms) RF: flip angle 8 degrees Acceleration: no SENSE inversion-prepared, inversion delay time: shortest Cheers, Jelmer Kok ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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