Maybe try running fslreorient2std before FreeSurfer. Peace,
Matt. On 11/15/12 8:55 AM, "Donna Dierker" <[email protected]> wrote: >The volumes look okay in AFNI, which doesn't warn about it being oblique. > They look like the captures. > >They are in what AFNI calls AIL orientation. Here is the nifti_tool >header output: > >it:/upload> nifti_tool -disp_hdr -infiles OrigT1w.nii.gz > >header file 'OrigT1w.nii.gz', num_fields = 43 > >all fields: > name offset nvals values > ------------------- ------ ----- ------ > sizeof_hdr 0 1 348 > data_type 4 10 > db_name 14 18 ?TR:7.412 TE:3.00 > extents 32 1 0 > session_error 36 1 0 > regular 38 1 r > dim_info 39 1 0 > dim 40 8 3 256 256 192 1 1 1 1 > intent_p1 56 1 0.0 > intent_p2 60 1 0.0 > intent_p3 64 1 0.0 > intent_code 68 1 0 > datatype 70 1 4 > bitpix 72 1 16 > slice_start 74 1 0 > pixdim 76 8 -1.0 1.0 1.0 1.0 0.007412 1.0 1.0 1.0 > vox_offset 108 1 352.0 > scl_slope 112 1 1.0 > scl_inter 116 1 0.0 > slice_end 120 1 0 > slice_code 122 1 0 > xyzt_units 123 1 10 > cal_max 124 1 0.0 > cal_min 128 1 0.0 > slice_duration 132 1 0.0 > toffset 136 1 0.0 > glmax 140 1 255 > glmin 144 1 0 > descrip 148 80 > aux_file 228 24 > qform_code 252 1 1 > sform_code 254 1 1 > quatern_b 256 1 0.5 > quatern_c 260 1 -0.5 > quatern_d 264 1 -0.5 > qoffset_x 268 1 -97.6138 > qoffset_y 272 1 150.709 > qoffset_z 276 1 -122.544998 > srow_x 280 4 0.0 0.0 1.0 -97.6138 > srow_y 296 4 -1.0 0.0 0.0 150.709 > srow_z 312 4 0.0 1.0 0.0 -122.544998 > intent_name 328 16 > magic 344 4 n+1 > >it:/upload> nifti_tool -disp_hdr -infiles T2w.nii.gz > >header file 'T2w.nii.gz', num_fields = 43 > >all fields: > name offset nvals values > ------------------- ------ ----- ------ > sizeof_hdr 0 1 348 > data_type 4 10 > db_name 14 18 > extents 32 1 0 > session_error 36 1 0 > regular 38 1 r > dim_info 39 1 0 > dim 40 8 3 256 256 192 1 1 1 1 > intent_p1 56 1 0.0 > intent_p2 60 1 0.0 > intent_p3 64 1 0.0 > intent_code 68 1 0 > datatype 70 1 4 > bitpix 72 1 16 > slice_start 74 1 0 > pixdim 76 8 -1.0 1.0 1.0 1.0 1.0 0.0 0.0 0.0 > vox_offset 108 1 352.0 > scl_slope 112 1 1.0 > scl_inter 116 1 0.0 > slice_end 120 1 0 > slice_code 122 1 0 > xyzt_units 123 1 10 > cal_max 124 1 0.0 > cal_min 128 1 0.0 > slice_duration 132 1 0.0 > toffset 136 1 0.0 > glmax 140 1 0 > glmin 144 1 0 > descrip 148 80 FSL4.1 > aux_file 228 24 > qform_code 252 1 1 > sform_code 254 1 1 > quatern_b 256 1 0.5 > quatern_c 260 1 -0.5 > quatern_d 264 1 -0.5 > qoffset_x 268 1 -97.6138 > qoffset_y 272 1 150.709 > qoffset_z 276 1 -122.544998 > srow_x 280 4 0.0 0.0 1.0 -97.6138 > srow_y 296 4 -1.0 0.0 0.0 150.709 > srow_z 312 4 0.0 1.0 0.0 -122.544998 > intent_name 328 16 > magic 344 4 n+1 > > >On Nov 15, 2012, at 4:38 AM, Yuichiro Shimizu <[email protected]> >wrote: > >> Hi, >> >> In my previous mail, I attached six pieces of screenshots. But their >> file sizes are too big and received a message from >> caret-users-bounces. >> Then, I uploaded the original T1w (OrigT1w.nii.gz), the original T2w >> (OrigT2w.nii.gz), and the converted T2w data (T2w.nii.gz) to the web >> site that Donna mentioned. >> Please examine them and tell me what is the problem. >> >> Thank you, >> >> Yuichiro Shimizu >> >> 2012/11/15 Donna Dierker <[email protected]> >>> >>> Hi Yuichiro, >>> >>> I think the most efficient thing is for you to upload your T1 & T2 >>>NIFTI volumes here: >>> >>> http://pulvinar.wustl.edu/cgi-bin/upload.cgi >>> >>> Just the original T1/T2. We can look at the header and see if Matt's >>>hunch was right. >>> >>> Donna >>> >>> >>> On Nov 14, 2012, at 3:45 AM, Yuichiro Shimizu <[email protected]> >>>wrote: >>> >>>> Thank you for your reply. >>>> >>>> I did the Caret Operation process for the downloaded data from NAMIC >>>>again. >>>> Then I found a typing error of file extension in the process. >>>> Correcting it, I could finally obtain the same figure as the Fig. 3 >>>>(Glasser et al. 2011). >>>> I'm very sorry for my careless mistake. >>>> >>>> myelin capture (file name: downloadeddata_myelin) >>>> thickness capture (file name: downloadeddata_thickness) >>>> >>>> But there still is a problem. >>>> When I analyzed the data that were taken in our MRI scanner in the >>>>same manner, >>>> the resultant MyelinMapping.metric files contain only the number, >>>>zero. >>>> (while thickness.metric contains plausible values) >>>> >>>> myelin capture (file name: mydata_myelin) >>>> thickness capture (file name: mydata_thickness) >>>> >>>> I compared all the resultant images in the process, i.e., T1w, >>>>OrigT2w, OrigT2w_conform_RAS, T2w_conform_RAS2T1wbb... >>>> Only one difference that I found is the direction of T1w, T2w images >>>>in FSLview. >>>> >>>> T1w FSLview / NAMIC (file name: downloadeddata_originalT1w) >>>> T2w FSLview / NAMIC (file name: downloadeddata_T2w) >>>> >>>> T1w FSLview / our data (file name: mydata_originalT1w) >>>> T2w FSLview / our data (file name: mydata_T2w) >>>> >>>> I wonder if the phase/frequency encoding caused the difference. >>>> Is there any other point I have to check or change? >>>> >>>> Sincerely. >>>> >>>> Yuichiro Shimizu >>>> >>>> 2012/11/13 Matt Glasser <[email protected]> >>>> I wonder if your sform has obliques in it. I agree that a screenshot >>>> would be helpful, together with verifying that the surfaces and T1w >>>>and >>>> T2w volumes are well aligned in some other screenshots. >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> On 11/12/12 8:42 AM, "Donna Dierker" <[email protected]> wrote: >>>> >>>>> Okay, if you're using a down sampled map (which might be in the >>>>>myelin >>>>> mapping pipeline -- just not sure), then all bets are off. I would >>>>>think >>>>> you'd need a downsampled spec file. Maybe one exists in sumsdb. Try >>>>> searching for the number of nodes you have. Use the "Show Parent" >>>>> feature from the sumsdb drop-down menu, if needed. >>>>> >>>>> It's not clear to me whether you did "File: Open Data File: Metric >>>>>file" >>>>> at any point. After adding the file to the spec file, and clicking >>>>>open, >>>>> it should have the same effect, but that was still hazy for me. But >>>>>it >>>>> is probably the resolution issue, as you say. >>>>> >>>>> There is variability in myelin maps, but your result sounds >>>>>suspicious. >>>>> Attach a capture. >>>>> >>>>> >>>>> On Nov 12, 2012, at 6:56 AM, 清水祐一郎 <[email protected]> wrote: >>>>> >>>>>> Thank you for a quick reply. >>>>>> >>>>>> I found and downloaded the files that you mentioned. >>>>>> Using the files, I've tried mapping. >>>>>> I added R.MyelinMapping.metric to the >>>>>> Fig4_fsaverage_Conte-69.164k_fs_LR.spec, and in the Display Control, >>>>>> tried to set the metric file. >>>>>> But, I couldn't find the metric file and overlay the >>>>>> R.MyelinMapping.metric onto the FIDUCIAL >>>>>> fsaverage.L.midthickness_mni.mws_flip-x.164k_fs_LR.coord.gii. >>>>>> >>>>>> On the other hand, I also tried mapping L.MyelinMapping.metric onto >>>>>>the >>>>>> left fiducial coordinates. >>>>>> >>>>>> I completely obeyed the process described in the website, >>>>>> CaretOperation, using the downloaded data. >>>>>> And then, I made a spec file below. >>>>>> First, I added the topo and coord files. >>>>>> There were topo.gii and coord.gii files so I renamed the files >>>>>>eraseing >>>>>> .gii. >>>>>> Then I changed the spec file's resolution. I set the number of >>>>>>nodes, >>>>>> 2562. >>>>>> Finally, I overlayed L.MyelinMapping.metric >>>>>> >>>>>> But, the myelin mapping pattern is different from the Figure 3 >>>>>>(Glasser >>>>>> et al. 2011). >>>>>> In Fig.3, the regions around the central sulcus and occipital lobe >>>>>>are >>>>>> strongly mylinated. >>>>>> But, the result that I obtained showed the pattern that the middle >>>>>>and >>>>>> upper part of >>>>>> the brain is myelinated. >>>>>> >>>>>> Is there any wrong procedure? >>>>>> >>>>>> >>>>>> Furthermore, I analyzed other images that were taken in our MRI >>>>>>scanner. >>>>>> >>>>>> MRI scanner (3 Tesla GE Healthcare Signa HDxt) >>>>>> T1w images: SPGR TR 7400 ms, TE 3 ms, TI 600 ms, FA = 10, FOV = 256 >>>>>>x >>>>>> 256, 1 mm slice >>>>>> T2w images: CUBE(XETA) TR 2500 ms, TE 80 ms, FOV = 256 x 256, 1 mm >>>>>> slice >>>>>> >>>>>> I obtained plausible thickness maps, but the intensity in >>>>>>myelin.metric >>>>>> are all zero! >>>>>> Although the scanning condition seems to be the same as the paper, >>>>>>the >>>>>> results are apparently wrong. >>>>>> I'm at a loss what is wrong. >>>>>> >>>>>> I appreciate your kindful instruction. >>>>>> >>>>>> Yuichiro Shimizu >>>>>> >>>>>> 2012/11/9 Donna Dierker <[email protected]> >>>>>> Matt might get to this, but here are some clues based on how I'd >>>>>> proceed in your shoes: >>>>>> >>>>>> Find a figure in one of our papers like the one I want to make, >>>>>>e.g.: >>>>>> >>>>>> >>>>>> >>>>>>http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8288739&archiv >>>>>>e_na >>>>>> me=Fig4_fsaverage_Conte-69.164k_fs_LR.spec >>>>>> >>>>>> (I couldn't find the sumsdb dir for Matt's myelin paper, but I think >>>>>> David's paper will work for the purposes of jumpstarting you into a >>>>>> visualization spec.) >>>>>> >>>>>> Fig 4D from the drop-down menu could just as easily have a myelin >>>>>>map >>>>>> overlaid on it. >>>>>> >>>>>> Download that spec and overlay your maps on the Conte69 inflated >>>>>> surface. >>>>>> >>>>>> This is probably not as step-by-step as you would like, but this >>>>>> happens to be a very busy time for everyone. If you run into >>>>>>trouble, >>>>>> post again. >>>>>> >>>>>> >>>>>> On Nov 9, 2012, at 12:31 AM, 清水祐一郎 <[email protected]> wrote: >>>>>> >>>>>>> Hello >>>>>>> >>>>>>> According to the web page Caret operation:MyelinMapping, I've >>>>>> obtained the final results: L.MyelinMapping.metric, >>>>>> R.MyelinMapping.metric, T1wdividedbyT2w.nii.gz, and >>>>>> T1wdividedbyT2w_ribbon.nii.gz. >>>>>>> The detail condition is described below. >>>>>>> >>>>>>> -information about my analysis procedure >>>>>>> individual MRI data: downloaded from NAMIC >>>>>>> recon-all by FreeSurfer(stable5-20110522) in CentOS5.5 64 bit >>>>>>> myelinmapping by Caret5 ver.5.65 in Windows7 64 bit >>>>>>> >>>>>>> Through the processes, no error message was displayed. >>>>>>> Furthermore, I confirmed that the T1wdividedbyT2w.nii.gz image is >>>>>> comparable with an other result image, the original T1w image >>>>>>divided by >>>>>> the registered T2w imageby by ImCalc in spm8. >>>>>>> >>>>>>> However, I have trouble in viewing the result of >>>>>>>MyelinMapping.metric >>>>>> on the inflated surface as shown in the paper (Glasser et al. 2012) >>>>>>> >>>>>>> When I try to open the L.MyelinMapping.metric, 'Creat Spec File' >>>>>> window is open. >>>>>>> I don't know how to make a spec file. >>>>>>> >>>>>>> Tentatively, I set the subject name and chose 'left' as the >>>>>>>structure. >>>>>>> Next, I pushed the OK button for 'creat new column' for left >>>>>>>smoothed >>>>>> corrected myelin map. >>>>>>> Finally, I got an error message, Error: L.MyelinMapping.metric: >>>>>> Contains different number of nodes than. >>>>>>> >>>>>>> In addition to this, I tried 'Add Document File to Spec File'. >>>>>>> I added a topo.file, a coord.file, and a structural 3D image. >>>>>>> It did not work, too. >>>>>>> >>>>>>> Because I'm a newcomer as Caret user, I'd like detailed >>>>>>>information. >>>>>>> >>>>>>> Thank you in advance. >>>>>>> >>>>>>> Yuichiro Shimizu >>>>>>> _______________________________________________ >>>>>>> caret-users mailing list >>>>>>> [email protected] >>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> caret-users mailing list >>>>>> [email protected] >>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>>> >>>>>> _______________________________________________ >>>>>> caret-users mailing list >>>>>> [email protected] >>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>> >>>>> >>>>> _______________________________________________ >>>>> caret-users mailing list >>>>> [email protected] >>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>> >>>> >>>> _______________________________________________ >>>> caret-users mailing list >>>> [email protected] >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>> >>>> >>>><downloadeddata_myelin.jpg><downloadeddata_originalT1w.jpg><downloadedd >>>>ata_T2w.jpg><downloadeddata_thickness.jpg><mydata_myelin.jpg><mydata_or >>>>iginalT1w.jpg><mydata_T2w.jpg><mydata_thickness.jpg>___________________ >>>>____________________________ >>>> caret-users mailing list >>>> [email protected] >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> >>> _______________________________________________ >>> caret-users mailing list >>> [email protected] >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > >_______________________________________________ >caret-users mailing list >[email protected] >http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
