Hi Bruce, I can view the file using "*freeview -v file.mnc*" but I think that won't solve my problem as I need to switch from 2D to 3D and vice versa. I will be thankful if you could be a bit specific about "preserving the direction cosine information" as I am facing difficulty to process these volumes through FS.
Thanks, Gunjan On Tue, Dec 16, 2014 at 7:59 AM, Gunjan Gautam <gunjan.gemin...@gmail.com> wrote: > > Thank you Bruce, > > I try this out. > On Dec 16, 2014 7:58 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > wrote: > >> I'm not sure what to tell you then. You need to save it in a format that >> preserves the direction cosine information. This shouldn't be that hard to >> do (e.g in matlab) >> Bruce >> >> >> On Tue, 16 Dec 2014, Gunjan Gautam wrote: >> >> >>> I think that won't resolve my issue because I need to deal with a >>> specific >>> set of noise removal algorithms and nonuniformity correction algorithms. >>> >>> On Dec 16, 2014 7:50 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> >>> wrote: >>> have you tried just giving the original volume to recon-all? We >>> typically deal with this kind of thing internally (and in 3D, >>> not on a slice-by-slice basis) >>> >>> cheers >>> Bruce >>> On Tue, 16 Dec 2014, Gunjan Gautam wrote: >>> >>> >>> Sure, >>> >>> My data(3D volume) is having different ranges of >>> noise and nonuniformity so >>> I want to apply different algorithms to get rid of >>> these and analyze the >>> extent. >>> >>> On Dec 16, 2014 7:40 AM, "Bruce Fischl" >>> <fis...@nmr.mgh.harvard.edu> wrote: >>> Hi Gunjan >>> can you elaborate? What kind of modifications >>> would you want to >>> make to each slice? >>> >>> Bruce >>> On Tue, 16 Dec 2014, Gunjan Gautam wrote: >>> >>> >>> Yes Bruce, minc is a volume but I want >>> to perform >>> some experiments and see >>> the aftereffects. >>> This is how I come from 3D to 2D to make >>> changes in >>> each slice and again I >>> rejoin these slices (2D to 3D). I don't >>> know if >>> anything other than NIfTi >>> gives this much flexibility or it could >>> be dealt >>> without coming in 2D space. >>> >>> Any suggestion will be highly >>> appreciate. >>> >>> On Dec 16, 2014 7:22 AM, "Bruce Fischl" >>> <fis...@nmr.mgh.harvard.edu> wrote: >>> isn't the minc a volume? It >>> certainly supports >>> holding an entire >>> volume in a single file >>> On Tue, 16 Dec 2014, Gunjan Gautam >>> wrote: >>> >>> >>> Ok , I try this out. >>> >>> I converted it to nii >>> because after >>> processing 2D >>> slices of the volume, I >>> can easily switch to 3D >>> space(ie >>> stacking) in order >>> to apply brain >>> extraction tools as NIfTi >>> provides some >>> of the >>> useful utilities. >>> >>> On Dec 16, 2014 6:59 AM, >>> "Bruce Fischl" >>> <fis...@nmr.mgh.harvard.edu> >>> wrote: >>> why do you need to >>> convert it to >>> nifti? Can >>> you process the minc >>> directly? See if >>> freeview can >>> display it: >>> >>> freeview -v file.mnc >>> >>> >>> >>> On Tue, 16 Dec 2014, >>> Gunjan Gautam >>> wrote: >>> >>> >>> Hi Bruce, >>> >>> Originally, data >>> was in MINC >>> format. >>> >>> On Dec 16, 2014 >>> 1:54 AM, >>> "Bruce Fischl" >>> >>> <fis...@nmr.mgh.harvard.edu> >>> wrote: >>> Hi Gunjan >>> >>> what was >>> the original >>> data format >>> that you >>> had? Once you >>> have >>> converted >>> it to nifti >>> in your >>> current stream >>> you can no >>> longer >>> use the >>> data, so you >>> have to start >>> further >>> upstream >>> >>> cheers >>> Bruce >>> >>> >>> On Tue, 16 >>> Dec 2014, >>> Gunjan Gautam >>> wrote: >>> >>> >>> I >>> don't have >>> dicom for this >>> subject but >>> it can >>> >>> easily be >>> converted to from >>> .nii >>> to .dcm. >>> I >>> try this out >>> and get back >>> to you if I >>> stuck at >>> some >>> point. >>> >>> >>> Thanks, >>> >>> Gunjan >>> >>> On >>> Dec 16, 2014 >>> 12:49 AM, >>> "Bruce Fischl" >>> >>> <fis...@nmr.mgh.harvard.edu> >>> wrote: >>> >>> do you >>> have the dicom >>> data for >>> this subject? >>> If >>> so, it will >>> be >>> >>> separated >>> into >>> different "series" >>> each >>> >>> corresponding to >>> one >>> >>> >>> acquisition (e.g. a >>> T1-weighted >>> one such as >>> >>> mprage or >>> FLASH). >>> >>> Typically >>> that series >>> will have >>> more than 150 >>> >>> slices (since >>> >>> that's >>> what it takes >>> to cover the >>> brain at >>> >>> close to 1mm >>> voxel >>> >>> size). You >>> need to >>> give recon-all >>> the dicom >>> file >>> that >>> contains a >>> >>> single one >>> of those >>> slices. It >>> doesn't matter >>> >>> which one - we >>> >>> will >>> figure out the >>> rest of them >>> from any of >>> them >>> >>> >>> On Tue, 16 >>> Dec 2014, >>> Gunjan Gautam >>> wrote: >>> >>> >>> >>> Hi >>> Bruce, >>> >>> >>> I am >>> sorry to >>> say that I did >>> not get you >>> >>> properly. >>> >>> >>> Could you please >>> say a bit >>> more about "a >>> >>> *single* >>> >>> >>> slice in the >>> correct >>> >>> >>> series ". I want >>> to try this >>> option. >>> >>> >>> On >>> Dec 16, 2014 >>> 12:13 AM, >>> "Bruce Fischl" >>> >>> >>> <fis...@nmr.mgh.harvard.edu> >>> wrote: >>> >>> >>> Hi Gunjan >>> >>> >>> >>> freesurfer >>> will handle >>> the dicom >>> >>> slices just >>> >>> >>> find. Just give >>> >>> >>> recon-all >>> a *single* >>> slice in the >>> >>> correct >>> >>> >>> series with the >>> -i >>> >>> >>> command >>> and it should >>> work. I >>> >>> don't know >>> >>> >>> medcon, but it >>> is not >>> >>> >>> >>> propagating the >>> direction cosine >>> info >>> into the >>> >>> >>> nifti, which >>> >>> >>> means that >>> the nifti >>> files are >>> >>> effectively >>> >>> >>> useless as you >>> will >>> >>> >>> never be >>> able to >>> distinguish left >>> from >>> right >>> >>> >>> again >>> >>> >>> >>> cheers >>> >>> >>> Bruce >>> >>> >>> >>> >>> On Tue, 16 >>> Dec 2014, >>> Gunjan Gautam >>> >>> wrote: >>> >>> >>> >>> >>> >>> Thanks Bruce, >>> >>> >>> >>> I >>> used "medcon" >>> command >>> >>> (Ubuntu) for the >>> >>> >>> stacking of >>> >>> >>> 2D >>> slices in >>> order to >>> >>> >>> >>> convert it in a >>> volume. >>> >>> These slices >>> >>> were >>> obtained >>> >>> >>> from >>> a volume >>> itself and >>> >>> >>> >>> after making >>> some intensity >>> >>> changes, a >>> >>> >>> volume is >>> >>> >>> >>> formed (using >>> medcon) >>> >>> >>> >>> again. Then I >>> fed this >>> >>> volume as input >>> >>> to >>> FS in >>> >>> >>> >>> order to extract >>> brain. >>> >>> >>> >>> Can >>> I overcome >>> this >>> >>> orientation >>> issue ? >>> >>> >>> >>> >>> Gunjan >>> >>> >>> >>> On >>> Dec 15, 2014 >>> 11:49 PM, >>> >>> "Bruce Fischl" >>> >>> >>> >>> >>> <fis...@nmr.mgh.harvard.edu> >>> >>> wrote: >>> >>> >>> >>> Hi Gunjan >>> >>> >>> >>> >>> the >>> problem is that >>> the >>> nifti >>> >>> >>> volume doesn't >>> >>> >>> >>> contain the >>> >>> >>> >>> direction >>> cosine >>> >>> information that >>> >>> we >>> need to >>> >>> >>> >>> figure out what >>> >>> >>> >>> directions >>> are A/P, >>> I/S >>> and L/R. >>> >>> >>> mri_convert >>> >>> >>> >>> warns of this: >>> >>> >>> >>> >>> >>> mri_convert >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> m000-stacks-m000-t1_icbm_normal_1mm_pn0_rf0-00001.nii.gz >>> >>> >>> >>> test.mgz >>> >>> >>> >>> >>> mri_convert >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> m000-stacks-m000-t1_icbm_normal_1mm_pn0_rf0-00001.nii.gz >>> >>> >>> >>> test.mgz >>> >>> >>> >>> $Id: >>> mri_convert.c,v >>> >>> 1.213 >>> >>> >>> 2014/07/29 >>> 19:22:31 >>> >>> >>> >>> fischl Exp $ >>> >>> >>> >>> reading >>> from >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> m000-stacks-m000-t1_icbm_normal_1mm_pn0_rf0-00001.nii.gz... >>> >>> >>> >>> WARNING: >>> neither >>> >>> NIfTI-1 qform or >>> >>> >>> sform are >>> >>> >>> >>> valid >>> >>> >>> >>> WARNING: >>> your volume >>> will >>> probably >>> >>> be >>> >>> >>> >>> incorrectly >>> oriented >>> >>> >>> >>> TR=1.00, >>> TE=0.00, >>> >>> TI=0.00, flip >>> >>> >>> angle=0.00 >>> >>> >>> >>> WARNING: >>> it does not >>> >>> appear that >>> >>> >>> there was >>> >>> >>> >>> sufficient >>> >>> >>> >>> >>> information >>> >>> >>> >>> in the >>> input to assign >>> >>> orientation >>> >>> to >>> the >>> >>> >>> >>> volume... >>> >>> >>> >>> i_ras = >>> (-1, 0, 0) >>> >>> >>> >>> j_ras = >>> (0, 1, 0) >>> >>> >>> >>> k_ras = >>> (0, 0, 1) >>> >>> >>> >>> writing to >>> test.mgz... >>> >>> >>> >>> >>> and if you >>> try to view >>> the >>> >>> >>> converted volume >>> in >>> >>> >>> >>> freeview it >>> shows >>> >>> >>> >>> up in the >>> wrong >>> >>> orientation (e.g >>> >>> what >>> we think >>> >>> >>> is >>> "coronal" is >>> >>> >>> >>> actually >>> horizonatal). >>> >>> >>> >>> >>> How did >>> you create the >>> >>> nifti >>> >>> >>> files? If you >>> >>> >>> give >>> dicom >>> directly >>> >>> >>> >>> to >>> recon-all you >>> will >>> >>> likely not >>> >>> have >>> this >>> >>> >>> >>> problem >>> >>> >>> >>> >>> cheers >>> >>> >>> >>> Bruce >>> >>> >>> >>> >>> >>> On Thu, 11 >>> Dec 2014, >>> >>> Gunjan Gautam >>> >>> >>> wrote: >>> >>> >>> >>> >>> ​Dear >>> all, >>> >>> >>> >>> >>> I am >>> facing few >>> >>> errors in >>> >>> >>> recon-all >>> >>> >> >> >> _______________________________________________ >> 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 . 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