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&archive_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><downloadeddata_T2w.jpg><downloadeddata_thickness.jpg><mydata_myelin.jpg><mydata_originalT1w.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
