Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Freesurfer Start Up
by Isaiah C. Smith 03 Aug '14

03 Aug '14

Hello All, I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated. Isaiah Smith

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Repost | Re: mni152reg error
by JacobML＠nmr.mgh.harvard.edu 02 Aug '14

02 Aug '14

Hello Doug, Ideally, I am trying to take subject tstat maps from FsFast (stable3 environment) and register these native structural space maps to the MNI152_2mm standard brain. The t_000.bfloat file is what was generated relative to my contrast that was set up in FsFast stable3. There are a series of these files ranging from t_000.bfloat to t_029.bfloat and there are also these same named files with a .hdr extension. t_000.bfloat is the file I designate when I select an overlay within tkmedit. Your help sorting out this registration is very appreciated. Thank you, Jacob >> I'm not sure what you are trying to do, but that command line looks like >> things are not set up properly. What is t_000.bfloat? (And why are you using bfloats?) >> doug >> On 7/17/14 1:14 PM, JacobML(a)nmr.mgh.harvard.edu wrote: >>> Hello again Doug, >>> Thank you for sending the updated version of mri152reg. It ran without error and generated the reg.mni152.2mm.dat registration matrix. Unfortunately though, when I tried to apply the transformation to the same >>> subject's t_000.bfloat, the registration is not correct (command below). mri_vol2vol --inv --targ /.../t_000.bfloat --mov >>> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o >>> CD_cerv_pat4_sess1_tstat1_MNI152.nii.gz --interp nearest --reg /.../CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat On a positive note, I was able to load the output image and >>> MNI152_T1_2mm.nii.gz within fslview, but the functional data seemed to be shifted too far anterior. >>> With my next attempt, I used mri_convert to make the t_000.bfloat into a .mgz and than ran mri_vol2vol, but the same misalignment occurred (see attached photo). >>> Using tkmedit, I have confirmed that this file aligns properly on this subject's native structural image, so I am not quite sure why the registration matrix may be off. Given that the reg.mni152.2mm.dat file reflects the transformation of the native struc to MNI, I wonder if I need >>> to account for the reg file between the func data and the native struc? >>> Can you please let me know what I may be doing incorrectly? >>> As always, your help is very appreciated. >>> Jacob >>>> Yea, i fixed this problem. I've attached a new version with the fix. doug >>>> On 07/17/2014 10:35 AM, JacobML(a)nmr.mgh.harvard.edu wrote: >>>>> Hello Freesurfer Experts, >>>>> I am trying to view stats generated with FsFast in fslview/MNIspace, >>> and >>>>> in doing so I have run mni152reg to generate the registration matrix. >>> That said, mni152reg did not complete correctly and below I have pasted >>> the terminal output: >>>>> Thu Jul 17 09:58:10 EDT 2014 >>>>> setenv SUBJECTS_DIR >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons >>>>> cd /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons >>> /usr/local/freesurfer/stable5_3_0/bin/mni152reg --s >>>>> CD_cerv_pat4_sess1_recon >>>>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 >>> UTC >>>>> 2014 x86_64 x86_64 x86_64 GNU/Linux >>>>> fslregister --mov >>>>> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz >>> --s CD_cerv_pat4_sess1_recon --reg >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat >>> --dof 12 >>>>> mkdir: cannot create directory >>>>> `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833': >>> Permission denied >>>>> Log file is >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat.fslregister.log >>> Thu Jul 17 09:58:11 EDT 2014 >>>>> --mov >>>>> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz >>> --s CD_cerv_pat4_sess1_recon --reg >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat >>> --dof 12 >>>>> $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ >>>>> purkinje >>>>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 >>> UTC >>>>> 2014 x86_64 x86_64 x86_64 GNU/Linux >>>>> nIters 1 >>>>> -------------------------------------- >>>>> /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons mri_convert >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz >>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii mri_convert >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz >>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii niiWrite(): error opening file >>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii >>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz... >>> TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00 >>>>> i_ras = (-1, 0, 0) >>>>> j_ras = (-0, -0, -1) >>>>> k_ras = (0, 1, 0) >>>>> writing to >>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii... >>> ERROR: failure writing >>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii >>> I tried to run the fslregister command from within the subject's directory >>>>> (in hopes to possible correct what may be a permissions issue), but >>> this >>>>> produces the same final error, "ERROR: failure writing >>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.24919/refvol.fslregister.nii." >>> Lastly, probably to no surprise, the >>>>> /.../mri/transforms/reg.mni152.2mm.dat file was never generated. Any >>> ideas how I may be able to correct these errors? >>>>> Thank you for the help! >>>>> Jacob >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> -- >>>> 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/ _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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High intensity blood vessels in children with meMPRAGE
by McLaughlin, Katie 01 Aug '14

01 Aug '14

Hi Doug, Bruce, et al. We've used the MGH meMPRAGE protocol successfully with children and adolescents previously on a Siemens 3T. I've recently moved to a new institution and am using the protocol on a Philips 3T Achieva scanner and we've been having a lot of issues with high-intensity blood vessels (appearing bright white and interfering with segmentation in FreeSurfer). Screenshot of an example attached. We have added some rest slabs/sat bands to the protocol to address this, but it hasn't fully solved the problem. I'm wondering if you have any recommendations about adjusting things in FreeSurfer to help us get better segmentation? Thanks for your thoughts on this, Kate

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QDEC Cluster Analysis
by Mohammed Goryawala 01 Aug '14

01 Aug '14

Hello All, I have some questions related to the qdec analysis I have run. 1. On running the qdec I see that FWHM is an input which changes cluster definition significantly. How would I choose the right FWHM for the analysis and can it be related to any imaging parameters? 2. Secondly, on completion of the qdec analysis I want to export the clusters created by the qdec analysis into a volumetric file (which I can later convert to .nii). Please also suggest a way that would let me only export clusters above a particular size threshold. Thank you very much in advance. Mohammed Goryawala Department of Radiology University of Miami, Miller School of Medicine

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GLM error in QDEC
by McLaughlin, Katie 01 Aug '14

01 Aug '14

Hi Doug et al, I'm trying to run an analysis in QDEC and continue to get an error that says that the QDEC GLM design creates 0 factors. I'm attaching my data table here as well as the output of QDEC. I've tried deleting all variables in my data file other than one and testing just that comparison, but no luck. Any thoughts are much appreciated. Thanks, Kate SUBJECTS_DIR is '/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/SAS/FreeSurfer/FS_5.3' Input table: /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat Subj#, SubjID, Data... 1 1009 c 2 1014 c 3 1032 c 4 1034 c 5 1041 m 6 1043 m 7 1047 c 8 1058 m 9 1077 c 10 1094 m 11 1096 c 12 1097 c 13 1099 c 14 1100 m 15 1114 m 16 1119 m 17 1123 m 18 1125 c 19 1126 c 20 1128 c 21 1134 c 22 1137 m 23 1139 m 24 1142 m 25 1143 m 26 1153 m 27 1154 m 28 1157 c 29 1158 m 30 1163 m 31 1165 m 32 1166 m 33 1167 m 34 1171 c 35 1173 c 36 1175 c 37 1176 c 38 1177 m 39 1178 m 40 1179 c 41 1180 c 42 1181 c 1 maltreatment discrete 2 1 c 2 m Continuous Factors: Mean: StdDev: ------------------- ----- ------- Number of subjects: 42 Number of factors: 1 (1 discrete, 0 continuous) Number of classes: 2 Number of regressors: 2 ============================================================ ERROR: QdecGlmDesign::Create: zero factors!

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grey matter density
by Qiongmin 01 Aug '14

01 Aug '14

Dear All, I wonder if there are any functions that can calculate the grey matter density of the vertices or in the ROI manner? I figured out that Freesurfer can give the thickness, area, volume, curv, but I can not find grey matter density anywhere. Thanks for any advice! Qiongmin

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Editing the pial surface
by Lindsay Gubernick 01 Aug '14

01 Aug '14

Hi, I am doing manual corrections of topological errors and am wondering if there is a way to bypass recomputing the surfaces as suggested by the topographical errors tutorial and instead doing some sort of manual editing of the pial surface. Does such an editing option exist? Thank you, Lindsay Gubernick

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Surface reconstruction and quality checks in atrophied temporal lobes
by Makaretz, Sara Johanna 01 Aug '14

01 Aug '14

I have a set of subjects with moderate to severe temporal lobe atrophy. Surfaces are generally good everywhere except for portions of temporal lobes. It seems like control points are usually helpful in cases with problematic temporal lobes (ie. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-July/039596.html) but I'm hesitant to add too many control points in areas with limited/no wm (aka severely atrophied areas) for risk of misidentifying gm as wm. My goal is to run a cortical thickness analysis and look specifically at the temporal lobes, so I want to process/troubleshoot the subjects in as similar a manner as possible and produce generally accurate thickness maps. Attached are three screenshots: 1. tl_subj_A.jpeg : a subject with cp added across several slices and -autorecon2-cp -autorecon3 reprocessing; pial missing some gm in both lobes 2. tl_subj_B.jpeg : a subject after standard recon-all; generally good wm/gm recognition; good wm recognition but poor gm recognition in temporal lobes 3. tl_subj_C.jpeg : a subject after standard recon-all; generally similar to tl_subj_B.jpeg, but surfaces really went rogue in part of the atrophied lobe Questions: - Is there a combination of flags that would help identify gm in the temporal lobes of most subjects while maintaining wm accuracy? - Any suggestions for adding cp (or other edits) in a semi-standard/efficient way that would still allow for a valid cortical thickness analysis? - What happened to the surfaces in subjects like the one in tl_subj_C.jpeg? - In terms of checking output quality for a cortical thickness analysis, would it be most useful to use QA Tools (https://surfer.nmr.mgh.harvard.edu/fswiki/QATools) or another method such as creating histograms from one of the stats files and looking for outliers? - (In general) How much quality checking / editing is appropriate for a cortical thickness study? Thank you for any suggestions and/or resources!! Sara

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Help with mris_convert
by Tara Miskovich 01 Aug '14

01 Aug '14

Hi all, I am trying to convert a group cluster to GIFTI (.gii) format. I just need some help running mris_convert. The example for a label to GIFTI is mris_convert --label lh.V1.label V1 lh.white lh.V1.label.gii I'm trying to figure out what is required here. I understand I put in the label after label and the output at the end, but in this example I am not sure what the V1 and lh.white are for. Thanks, Tara

1 0

YANQ follow-up
by Krieger, Donald N. 01 Aug '14

01 Aug '14

Thanks again for the pointer, Bruce. You wrote: ... mri_convert -rl rawavg.mgz <input vol> <output vol> which does produce an output volume from which I now need to extract RAS voxel coordinates. A pointer to a keyboard command would be most welcome. Of interest is the difference between the color mappings for the input and output volumes in freeview. When using the lookup table in freeview they are quite different whereas in grayscale they are almost identical. I wonder if this is contributing to my difficulty in finding a tool to extract the voxel coordinates. Thanks again. Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text

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