Re: [Freesurfer] Fwd: Errors in recon-all
Ok I try this out using MATLAB. Thanks Bruce, On Wed, Dec 17, 2014 at 7:32 PM, Bruce Fischl wrote: > > Hi Gunjan > > I can't help you preserve it in minc and using someone else's tools to > convert slices to nifti. Can you work in matlb instead? If so, you can > convert the minc to .mgz with mri_convert, then load the mgz into matlab > using either MRIread or load_mgh (which will both return the direction > cosines), and save them with either MRIwrite or save_mgh, given preserving > the direction info. > > cheers > Bruce > > On Wed, 17 Dec 2014, Gunjan Gautam wrote: > > Hi Bruce, >> >> I am sorry that you could not get me properly. >> My query is, how can I preserve direction cosine information. As I am new >> to >> this issue, any help would really be appreciated. >> >> Thanks, >> Gunjan >> >> On Wed, Dec 17, 2014 at 7:08 PM, Bruce Fischl > > >> wrote: >> Hi Gunjan >> >> our coordinate systems are extensively documented here: >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems? >> action=AttachFil >> e&do=get&target=fscoordinates.ppt >> >> cheers >> Bruce >> >> On Wed, 17 Dec 2014, Gunjan Gautam wrote: >> >> 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 >> >> wrote: >> >> Thank you Bruce, >> >> I try this out. >> >> On Dec 16, 2014 7:58 AM, "Bruce Fischl" >>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" >> 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" >> >> wrote: >> Hi Gunjan >> can you elaborate? >> What kind >> of modifications >> would you want to >> make
Re: [Freesurfer] Fwd: Errors in recon-all
Hi Bruce, I am sorry that you could not get me properly. My query is, how can I preserve direction cosine information. As I am new to this issue, any help would really be appreciated. Thanks, Gunjan On Wed, Dec 17, 2014 at 7:08 PM, Bruce Fischl wrote: > > Hi Gunjan > > our coordinate systems are extensively documented here: > > http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems? > action=AttachFile&do=get&target=fscoordinates.ppt > > cheers > Bruce > > On Wed, 17 Dec 2014, Gunjan Gautam wrote: > > 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 > > >> wrote: >> >> Thank you Bruce, >> >> I try this out. >> >> On Dec 16, 2014 7:58 AM, "Bruce Fischl" >>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" >> 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" >> >> 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" >> >> wrote: >> isn't the minc a >> volume? It >> certainly supports >>
Re: [Freesurfer] Fwd: Errors in recon-all
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 wrote: > > Thank you Bruce, > > I try this out. > On Dec 16, 2014 7:58 AM, "Bruce Fischl" > 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" >>> 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" >>> 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" >>> 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" >>> >>> wrote: >>> why do you need to >>> convert it to >>> nifti? Can >>> you process the minc >>> directly? See if
Re: [Freesurfer] Fwd: Errors in recon-all
Thank you Bruce, I try this out. On Dec 16, 2014 7:58 AM, "Bruce Fischl" 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" >> 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" >> 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" >> 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" >> >> 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" >> >> >>
Re: [Freesurfer] Fwd: Errors in recon-all
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" 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" >> 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" >> 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" >> 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" >> >> 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 >>
Re: [Freesurfer] Fwd: Errors in recon-all
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" 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" >> 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" >> 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" >> 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" >> >> 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 >> t
Re: [Freesurfer] Fwd: Errors in recon-all
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" 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" >> 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" >> 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" >> 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" >> >> wrote: >> Hi Gunjan >> >> freesurfer will handle >> the dicom >> slices just >> find. Just give >>
Re: [Freesurfer] Fwd: Errors in recon-all
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" 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" >> 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" >> 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" >> 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 med
Re: [Freesurfer] Fwd: Errors in recon-all
Hi Bruce, Originally, data was in MINC format. On Dec 16, 2014 1:54 AM, "Bruce Fischl" 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" >> 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" >> 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" >> 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_rf0-1.nii.gz >> test.mgz >> mri_convert >> >> >> m000-stacks-m000-t1_icbm_normal_1mm_pn0_rf0-1.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_rf0-1.nii.gz... >> WARNING: neither N
Re: [Freesurfer] Fwd: Errors in recon-all
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" 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" >> 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" >> 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_rf0-1.nii.gz >> test.mgz >> mri_convert >> >> m000-stacks-m000-t1_icbm_normal_1mm_pn0_rf0-1.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_rf0-1.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 >> command (eg >
Re: [Freesurfer] Fwd: Errors in recon-all
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" 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" >> 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_rf0-1.nii.gz >> test.mgz >> mri_convert >> m000-stacks-m000-t1_icbm_normal_1mm_pn0_rf0-1.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_rf0-1.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 command (eg >> mritotal failed) while >> dealing with a specific set of volumes. How to >> overcome these issues in >> order to run recon-all successfully. >> Please find the recon-all.log and volume attached >> with this mail. >> >> Gunjan >> >> >> >> >> >> >> >> >> >> ___ >> 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 . 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. >> >> >> > ___ > 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 . 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. > > ___ 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 . 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.
Re: [Freesurfer] Fwd: Errors in recon-all
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" 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_rf0-1.nii.gz > test.mgz > mri_convert m000-stacks-m000-t1_icbm_normal_1mm_pn0_rf0-1.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_rf0-1.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 command (eg mritotal failed) while >> dealing with a specific set of volumes. How to overcome these issues in >> order to run recon-all successfully. >> Please find the recon-all.log and volume attached with this mail. >> >> Gunjan >> >> >> >> >> >> >> >> >> > ___ > 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 . 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. > > ___ 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 . 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.
Re: [Freesurfer] Number of slices generated in the brainmask.mgz
Thanks Eugenio, It worked. On Mon, Dec 1, 2014 at 7:11 PM, Eugenio Iglesias wrote: > Hi Gunjan, > if what you're trying to do is to bring brainmask.mgz to the native voxel > space of your input scan, you can run > mri_convert brainmask.mgz brainmaskResampled.nii.gz -rl input.nii.gz > where input.nii.gz is the scan you fed to FreeSurfer's recon-all (e.g., > recon-all -i input.nii.gz -s ) > Cheers, > /Eugenio > > Juan Eugenio Iglesias > Postdoctoral researcher BCBL > www.jeiglesias.com > www.bcbl.eu > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > > - Original Message - > From: "Gunjan Gautam" > To: "Freesurfer support list" > Sent: Monday, December 1, 2014 2:23:12 PM > Subject: [Freesurfer] Number of slices generated in the brainmask.mgz > > > > > > Hi FreeSurfers, > > brainmask.mgz is generating 256 slides per volume. How can I have control > over it, in terms of generating less number of slides (say 181) per volume? > > Gunjan > > ___ > 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 . 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. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ 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 . 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.
[Freesurfer] Number of slices generated in the brainmask.mgz
Hi FreeSurfers, brainmask.mgz is generating 256 slides per volume. How can I have control over it, in terms of generating less number of slides (say 181) per volume? Gunjan ___ 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 . 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.
Re: [Freesurfer] Regarding recon-all
Hi Bruce, What about the voxels having value equal to 5 (if exists) ? Gunjan On Sun, Nov 23, 2014 at 10:39 PM, Gunjan Gautam wrote: > Ok thank you Bruce > On Nov 23, 2014 10:37 PM, "Bruce Fischl" > wrote: > >> we don't have a binary one, but all voxels in brainmask.mgz that are >5 >> are in brain and everything <5 is not in brain >> >> cheers >> Bruce >> >> On Sun, 23 Nov 2014, Gunjan Gautam wrote: >> >> >>> Thanks, >>> >>> And what about the binary brain mask? I am able to see only the stripped >>> volume but need the binary brain mask as well. >>> >>> Gunjan >>> >>> On Nov 23, 2014 8:49 PM, "Bruce Fischl" >>> wrote: >>> Hi Gunjan >>> >>> 15 min is about what it is going to take. You could do it faster >>> but then the failure rate would go up. We've tuned it to improve >>> automaticity and reduce failures quite a bit. >>> >>> cheers >>> Bruce >>> >>> >>> On Sat, 22 Nov 2014, Gunjan Gautam wrote: >>> >>> >>> Hi, >>> >>> I used recon-all with all and its taking a lot of >>> time. My main concern is >>> only to get the stripped brain. >>> I tried with autorecon1 as well but its also taking >>> not less than 15min and >>> I need to deal with a huge data. >>> Last stage of autorecon1 is skull stripping which >>> takes the NU corrected >>> input (as it FS works as a pipeline). Is there any >>> way to directly get the >>> "stripped brain" and its binary mask. >>> >>> I also need to ask, which file of the output (name >>> with extension) is the >>> "binary brain mask" ? >>> >>> Best regards, >>> Gunjan >>> >>> >>> >>> ___ >>> 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 . 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. >>> >>> >>> >> ___ >> 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 . 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. >> >> ___ 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 . 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.
Re: [Freesurfer] Regarding recon-all
Ok thank you Bruce On Nov 23, 2014 10:37 PM, "Bruce Fischl" wrote: > we don't have a binary one, but all voxels in brainmask.mgz that are >5 > are in brain and everything <5 is not in brain > > cheers > Bruce > > On Sun, 23 Nov 2014, Gunjan Gautam wrote: > > >> Thanks, >> >> And what about the binary brain mask? I am able to see only the stripped >> volume but need the binary brain mask as well. >> >> Gunjan >> >> On Nov 23, 2014 8:49 PM, "Bruce Fischl" >> wrote: >> Hi Gunjan >> >> 15 min is about what it is going to take. You could do it faster >> but then the failure rate would go up. We've tuned it to improve >> automaticity and reduce failures quite a bit. >> >> cheers >> Bruce >> >> >> On Sat, 22 Nov 2014, Gunjan Gautam wrote: >> >> >> Hi, >> >> I used recon-all with all and its taking a lot of >> time. My main concern is >> only to get the stripped brain. >> I tried with autorecon1 as well but its also taking >> not less than 15min and >> I need to deal with a huge data. >> Last stage of autorecon1 is skull stripping which >> takes the NU corrected >> input (as it FS works as a pipeline). Is there any >> way to directly get the >> "stripped brain" and its binary mask. >> >> I also need to ask, which file of the output (name >> with extension) is the >> "binary brain mask" ? >> >> Best regards, >> Gunjan >> >> >> >> ___ >> 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 . 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. >> >> >> > ___ > 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 . 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. > > ___ 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 . 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.
Re: [Freesurfer] Regarding recon-all
Thanks, And what about the binary brain mask? I am able to see only the stripped volume but need the binary brain mask as well. Gunjan On Nov 23, 2014 8:49 PM, "Bruce Fischl" wrote: > Hi Gunjan > > 15 min is about what it is going to take. You could do it faster but then > the failure rate would go up. We've tuned it to improve automaticity and > reduce failures quite a bit. > > cheers > Bruce > > > On Sat, 22 Nov 2014, Gunjan Gautam wrote: > > >> Hi, >> >> I used recon-all with all and its taking a lot of time. My main concern is >> only to get the stripped brain. >> I tried with autorecon1 as well but its also taking not less than 15min >> and >> I need to deal with a huge data. >> Last stage of autorecon1 is skull stripping which takes the NU corrected >> input (as it FS works as a pipeline). Is there any way to directly get the >> "stripped brain" and its binary mask. >> >> I also need to ask, which file of the output (name with extension) is the >> "binary brain mask" ? >> >> Best regards, >> Gunjan >> >> >> > ___ > 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 . 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. > > ___ 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 . 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.
[Freesurfer] Regarding recon-all
Hi, I used recon-all with all and its taking a lot of time. My main concern is only to get the stripped brain. I tried with autorecon1 as well but its also taking not less than 15min and I need to deal with a huge data. Last stage of autorecon1 is skull stripping which takes the NU corrected input (as it FS works as a pipeline). Is there any way to directly get the "stripped brain" and its binary mask. I also need to ask, which file of the output (name with extension) is the "binary brain mask" ? Best regards, Gunjan ___ 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 . 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.
Re: [Freesurfer] Regarding mri_convert command
I downloaded two volumes from BrainWeb database. One is treated as ground truth because it has preassigned values(0-11) for each types of tissues and by a simple coding binary brain mask can be achieved. Another volume is the processed one using any brain extraction algorithm. Now, I have two volume one is standard and another processed one. I want to observe the performance of the algorithm that how much accurate which needs to compare both the volumes, pixel by pixel. This comparison will take place properly only when both volumes will generate same number of slides. I am stuck here. Now, ground truth is generating equal number of slides as of the processed volume but these are getting cropped (please see the attached jpg file in previous mail) . Hi Gunjan you need to give us more information. What are the two volumes? Why is one "ground truth"? What in general are you trying to achieve? cheers Bruce On Wed, 19 Nov 2014, Gunjan Gautam wrote: > I have attached both the volumes (reference and input) with my mail. > Its the last step of my work, I'm stuck at and not finding any solution. I > read that FreeSurfer can solve my problem. > > I will be obliged if you find some time for this. > > Best Regards, > Gunjan > > On Nov 19, 2014 8:19 PM, "Bruce Fischl" > wrote: > no, because I don't know what the volume are that you are using > On Wed, 19 Nov 2014, Gunjan Gautam wrote: > > > Ok I try this out. > > Did you answer my Query 1(related to cropped output > of mri_convert command ? > I probably did not understand. > > On Nov 19, 2014 8:10 PM, "Bruce Fischl" > wrote: > Hi Gunjan > > FreeSurfer has been designed to work as a > pipeline. Picking out > individual pieces and running them may or may > not work, and > certainly won't be as reliable. I would advise > you to run > recon-all -all, then you can use the contents > of the subject > directory to do whatever analyses you want > (e.g. generate an > un-bias-corrected, skull stripped volume). > > The subject id is one that you make up - it > will be the name of > the directory under which the results are > stored. Also specify a > SUBJECTS_DIR on the command line, which will > be the root > directory under which all the individual > subject trees live > (with -sd > > cheers > Bruce > > > On Wed, 19 Nov 2014, Gunjan Gautam wrote: > > Actually, I have two volumes, belong to > the same > subject. One volume is the > ground truth which will be considered as > standard > for the second volume > which is the processed one or the > extracted brain. > To perform a perfect > comparison between both volumes, these > must generate > equal number of slices > in order to compare the corresponding > slide. But > here there is problem with > my volumes, that is while performing > slicing Ground > Truth volume is > generating 360 slice and processed > volume is > generating 181 slides. So > comparison can't take place in this way. > This is the > reason I used > mri_convert command. > > > If I am not wrong then recon-all command > will do > bias correction as well, > which is not my requirement. What I want > is to have > the binary brain mask > volume and brain volume only. recon-all > command is > asking for the subject-id > and I'm not sure about it. I have gone > through its > documentation but still > not able to run it properly. I request > you to please > help me in this. > >
Re: [Freesurfer] Regarding mri_convert command
I have attached both the volumes (reference and input) with my mail. Its the last step of my work, I'm stuck at and not finding any solution. I read that FreeSurfer can solve my problem. I will be obliged if you find some time for this. Best Regards, Gunjan On Nov 19, 2014 8:19 PM, "Bruce Fischl" wrote: > no, because I don't know what the volume are that you are using > On Wed, 19 Nov 2014, Gunjan Gautam wrote: > > >> Ok I try this out. >> >> Did you answer my Query 1(related to cropped output of mri_convert >> command ? >> I probably did not understand. >> >> On Nov 19, 2014 8:10 PM, "Bruce Fischl" >> wrote: >> Hi Gunjan >> >> FreeSurfer has been designed to work as a pipeline. Picking out >> individual pieces and running them may or may not work, and >> certainly won't be as reliable. I would advise you to run >> recon-all -all, then you can use the contents of the subject >> directory to do whatever analyses you want (e.g. generate an >> un-bias-corrected, skull stripped volume). >> >> The subject id is one that you make up - it will be the name of >> the directory under which the results are stored. Also specify a >> SUBJECTS_DIR on the command line, which will be the root >> directory under which all the individual subject trees live >> (with -sd >> >> cheers >> Bruce >> >> >> On Wed, 19 Nov 2014, Gunjan Gautam wrote: >> >> Actually, I have two volumes, belong to the same >> subject. One volume is the >> ground truth which will be considered as standard >> for the second volume >> which is the processed one or the extracted brain. >> To perform a perfect >> comparison between both volumes, these must generate >> equal number of slices >> in order to compare the corresponding slide. But >> here there is problem with >> my volumes, that is while performing slicing Ground >> Truth volume is >> generating 360 slice and processed volume is >> generating 181 slides. So >> comparison can't take place in this way. This is the >> reason I used >> mri_convert command. >> >> >> If I am not wrong then recon-all command will do >> bias correction as well, >> which is not my requirement. What I want is to have >> the binary brain mask >> volume and brain volume only. recon-all command is >> asking for the subject-id >> and I'm not sure about it. I have gone through its >> documentation but still >> not able to run it properly. I request you to please >> help me in this. >> >> Regards, >> Gunjan >> >> >> On Wed, Nov 19, 2014 at 6:50 PM, Bruce Fischl >> >> wrote: >> Hi Gunjan >> >> you need to give us more details. What are you >> trying to do? Why >> not just run recon-all -all? That will be much >> easier than >> trying to ru individual steps >> >> chers >> Bruce >> >> On Wed, 19 Nov 2014, Gunjan Gautam wrote: >> >> Hi, >> >> I am facing few issues. I will be >> thankful if you >> can help me out. >> >> Query 1) I used "mri_convert a.nii >> a.resliced.nii >> -rl b.nii" in order to >> generate slices so that comparison may >> take place >> properly. The command ran >> properly but generating cropped slices. >> I am attaching the input volume, >> reference volume >> and the cropped slice >> screenshot. >> [icon_10_generic_list.png] a.nii >> >> [icon_10_generic_list.png] b.nii >> >> >> Query 2) For skull stripping I ran below >> co
Re: [Freesurfer] Regarding mri_convert command
Ok I try this out. Did you answer my Query 1(related to cropped output of mri_convert command ? I probably did not understand. On Nov 19, 2014 8:10 PM, "Bruce Fischl" wrote: > Hi Gunjan > > FreeSurfer has been designed to work as a pipeline. Picking out individual > pieces and running them may or may not work, and certainly won't be as > reliable. I would advise you to run recon-all -all, then you can use the > contents of the subject directory to do whatever analyses you want (e.g. > generate an un-bias-corrected, skull stripped volume). > > The subject id is one that you make up - it will be the name of the > directory under which the results are stored. Also specify a SUBJECTS_DIR > on the command line, which will be the root directory under which all the > individual subject trees live (with -sd > > cheers > Bruce > > > On Wed, 19 Nov 2014, Gunjan Gautam wrote: > > Actually, I have two volumes, belong to the same subject. One volume is >> the >> ground truth which will be considered as standard for the second volume >> which is the processed one or the extracted brain. To perform a perfect >> comparison between both volumes, these must generate equal number of >> slices >> in order to compare the corresponding slide. But here there is problem >> with >> my volumes, that is while performing slicing Ground Truth volume is >> generating 360 slice and processed volume is generating 181 slides. So >> comparison can't take place in this way. This is the reason I used >> mri_convert command. >> >> >> If I am not wrong then recon-all command will do bias correction as well, >> which is not my requirement. What I want is to have the binary brain mask >> volume and brain volume only. recon-all command is asking for the >> subject-id >> and I'm not sure about it. I have gone through its documentation but still >> not able to run it properly. I request you to please help me in this. >> >> Regards, >> Gunjan >> >> >> On Wed, Nov 19, 2014 at 6:50 PM, Bruce Fischl > > >> wrote: >> Hi Gunjan >> >> you need to give us more details. What are you trying to do? Why >> not just run recon-all -all? That will be much easier than >> trying to ru individual steps >> >> chers >> Bruce >> >> On Wed, 19 Nov 2014, Gunjan Gautam wrote: >> >> Hi, >> >> I am facing few issues. I will be thankful if you >> can help me out. >> >> Query 1) I used "mri_convert a.nii a.resliced.nii >> -rl b.nii" in order to >> generate slices so that comparison may take place >> properly. The command ran >> properly but generating cropped slices. >> I am attaching the input volume, reference volume >> and the cropped slice >> screenshot. >> [icon_10_generic_list.png] a.nii >> >> [icon_10_generic_list.png] b.nii >> >> >> Query 2) For skull stripping I ran below command >> bibl04@BIBL04:~/Desktop/freesurfer/bin$ recon-all >> -i a.nii -autorecon1 >> and its showing error for subject id. I am really >> not aware, what to write. >> ERROR: must specify a subject id >> >> Query 3) I did not find that which option from (1 >> to 31 ) should generate >> the "binary brain mask". >> >> >> Thanks, >> Gunjan >> >> On Wed, Nov 19, 2014 at 12:41 AM, Gunjan Gautam >> >> wrote: >> >> Ok, I go through that. >> >> Thanks, >> Gunjan >> >> On Nov 19, 2014 12:37 AM, "Bruce Fischl" >>wrote: >> Hi Gunjan, >> >> it's all on the wiki. You should go >> through our >> tutorials >> >> cheers >> Bruce >> On Wed, 19 Nov 2014, Gunjan Gautam >> wrote: >> >> >> Thank you >> >> I will be thankful if you could >> let me >> know
Re: [Freesurfer] Regarding mri_convert command
Actually, I have two volumes, belong to the same subject. One volume is the ground truth which will be considered as standard for the second volume which is the processed one or the extracted brain. To perform a perfect comparison between both volumes, these must generate equal number of slices in order to compare the corresponding slide. But here there is problem with my volumes, that is while performing slicing Ground Truth volume is generating 360 slice and processed volume is generating 181 slides. So comparison can't take place in this way. This is the reason I used mri_convert command. If I am not wrong then recon-all command will do bias correction as well, which is not my requirement. What I want is to have the binary brain mask volume and brain volume only. recon-all command is asking for the subject-id and I'm not sure about it. I have gone through its documentation but still not able to run it properly. I request you to please help me in this. Regards, Gunjan On Wed, Nov 19, 2014 at 6:50 PM, Bruce Fischl wrote: > Hi Gunjan > > you need to give us more details. What are you trying to do? Why not just > run recon-all -all? That will be much easier than trying to ru individual > steps > > chers > Bruce > > On Wed, 19 Nov 2014, Gunjan Gautam wrote: > > Hi, >> >> I am facing few issues. I will be thankful if you can help me out. >> >> Query 1) I used "mri_convert a.nii a.resliced.nii -rl b.nii" in order to >> generate slices so that comparison may take place properly. The command >> ran >> properly but generating cropped slices. >> I am attaching the input volume, reference volume and the cropped slice >> screenshot. >> [icon_10_generic_list.png] a.nii >> >> [icon_10_generic_list.png] b.nii >> >> >> >> Query 2) For skull stripping I ran below command >> bibl04@BIBL04:~/Desktop/freesurfer/bin$ recon-all -i a.nii -autorecon1 >> and its showing error for subject id. I am really not aware, what to >> write. >> ERROR: must specify a subject id >> >> Query 3) I did not find that which option from (1 to 31 ) should generate >> the "binary brain mask". >> >> >> Thanks, >> Gunjan >> >> On Wed, Nov 19, 2014 at 12:41 AM, Gunjan Gautam < >> gunjan.gemin...@gmail.com> >> wrote: >> >> Ok, I go through that. >> >> Thanks, >> Gunjan >> >> On Nov 19, 2014 12:37 AM, "Bruce Fischl" >>wrote: >> Hi Gunjan, >> >> it's all on the wiki. You should go through our >> tutorials >> >> cheers >> Bruce >> On Wed, 19 Nov 2014, Gunjan Gautam wrote: >> >> >> Thank you >> >> I will be thankful if you could let me >> know about the link related to >> recon-all, in order to know about the >> parameters(input volume info etc) >> associated to it and other usage. >> >> On Nov 19, 2014 12:18 AM, "Bruce Fischl" >>wrote: >> Hi Gunjan >> >> just run recon-all and it will do >> everything that we know how to >> do (including those steps) >> >> cheers >> Bruce >> On Wed, 19 Nov 2014, Gunjan Gautam >> wrote: >> >> >> Ok, I try this tomorrow >> morning. >> >> I will be thankful if you >> could tell me about >> getting brain mask and >> performing skull stripping >> otherwise I'll have to >> wait for 12 hours to get >> your replies as our working >> hours doesn't match. >> >> On Nov 18, 2014 8:45 PM, "Z >> K" >> >>wrote: >> Gunjan, this may be >> related to an Ubuntu >> specific issue we >> address on >> the Freesurfer >> download page: >> >>
Re: [Freesurfer] Regarding mri_convert command
Ok, I go through that. Thanks, Gunjan On Nov 19, 2014 12:37 AM, "Bruce Fischl" wrote: > Hi Gunjan, > > it's all on the wiki. You should go through our tutorials > > cheers > Bruce > On Wed, 19 Nov 2014, Gunjan Gautam wrote: > > >> Thank you >> >> I will be thankful if you could let me know about the link related to >> recon-all, in order to know about the parameters(input volume info etc) >> associated to it and other usage. >> >> On Nov 19, 2014 12:18 AM, "Bruce Fischl" >> wrote: >> Hi Gunjan >> >> just run recon-all and it will do everything that we know how to >> do (including those steps) >> >> cheers >> Bruce >> On Wed, 19 Nov 2014, Gunjan Gautam wrote: >> >> >> Ok, I try this tomorrow morning. >> >> I will be thankful if you could tell me about >> getting brain mask and >> performing skull stripping otherwise I'll have to >> wait for 12 hours to get >> your replies as our working hours doesn't match. >> >> On Nov 18, 2014 8:45 PM, "Z K" >> wrote: >> Gunjan, this may be related to an Ubuntu >> specific issue we >> address on >> the Freesurfer download page: >> >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/Download >> >> Specifically the part thats states the >> following: >> >> *** >> On Ubuntu, you might have to do this if qdec >> or freeview >> complain about >> libjpeg or libtiff: >> >> cd /usr/lib (/usr/lib/i386 or /usr/lib/x86_64 >> on some Ubuntu >> distros) >> sudo ln -s libjpeg.so.8 libjpeg.so.62 >> sudo ln -s libtiff.so.4 libtiff.so.3 >> *** >> >> -Zeke >> >> >> >> >> On 11/18/2014 03:55 AM, Gunjan Gautam wrote: >> > Hello Sir, >> > >> > I have place the "license.txt" in the same >> directory that >> contains >> > build-stamp.txt as there were no directory >> with name >> "FREESURFER_HOME". >> > freeview command is not working and showing >> below message >> > "freeview.bin: error while loading shared >> libraries: >> libjpeg.so.62: >> > cannot open shared object file: No such file >> or directory". >> > What next I need to do in order to generate >> a output brain >> mask. >> > >> > Best Regards, >> > Gunjan >> > >> > >> > >> > On Thu, Nov 13, 2014 at 12:24 AM, Z K >> > > <mailto:zkauf...@nmr.mgh.harvard.edu>> >> wrote: >> > >> > Im having a little difficulty following >> all the avenues of >> your attempts >> > to get this working, but the bottom line >> is that the error >> message below >> > is complaining that you do not have a >> valid license file. >> > >> > You need to go to this page and register >> and get the valid >> license file: >> > >> > >> https://surfer.nmr.mgh.harvard.edu/registration.html >> > >> > Once you get a valid license file you >> will need to place >> it in your >> > $FREESURFER_HOME directory (the same >> directory that >> contains >> > build-stamp.txt) and give it the name >> .l
Re: [Freesurfer] Regarding mri_convert command
Thank you I will be thankful if you could let me know about the link related to recon-all, in order to know about the parameters(input volume info etc) associated to it and other usage. On Nov 19, 2014 12:18 AM, "Bruce Fischl" wrote: > Hi Gunjan > > just run recon-all and it will do everything that we know how to do > (including those steps) > > cheers > Bruce > On Wed, 19 Nov 2014, Gunjan Gautam wrote: > > >> Ok, I try this tomorrow morning. >> >> I will be thankful if you could tell me about getting brain mask and >> performing skull stripping otherwise I'll have to wait for 12 hours to >> get >> your replies as our working hours doesn't match. >> >> On Nov 18, 2014 8:45 PM, "Z K" wrote: >> Gunjan, this may be related to an Ubuntu specific issue we >> address on >> the Freesurfer download page: >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/Download >> >> Specifically the part thats states the following: >> >> *** >> On Ubuntu, you might have to do this if qdec or freeview >> complain about >> libjpeg or libtiff: >> >> cd /usr/lib (/usr/lib/i386 or /usr/lib/x86_64 on some Ubuntu >> distros) >> sudo ln -s libjpeg.so.8 libjpeg.so.62 >> sudo ln -s libtiff.so.4 libtiff.so.3 >> *** >> >> -Zeke >> >> >> >> >> On 11/18/2014 03:55 AM, Gunjan Gautam wrote: >> > Hello Sir, >> > >> > I have place the "license.txt" in the same directory that >> contains >> > build-stamp.txt as there were no directory with name >> "FREESURFER_HOME". >> > freeview command is not working and showing below message >> > "freeview.bin: error while loading shared libraries: >> libjpeg.so.62: >> > cannot open shared object file: No such file or directory". >> > What next I need to do in order to generate a output brain >> mask. >> > >> > Best Regards, >> > Gunjan >> > >> > >> > >> > On Thu, Nov 13, 2014 at 12:24 AM, Z K >> > > <mailto:zkauf...@nmr.mgh.harvard.edu>> wrote: >> > >> > Im having a little difficulty following all the avenues of >> your attempts >> > to get this working, but the bottom line is that the error >> message below >> > is complaining that you do not have a valid license file. >> > >> > You need to go to this page and register and get the valid >> license file: >> > >> > https://surfer.nmr.mgh.harvard.edu/registration.html >> > >> > Once you get a valid license file you will need to place >> it in your >> > $FREESURFER_HOME directory (the same directory that >> contains >> > build-stamp.txt) and give it the name .license or >> license.txt. Try both. >> > >> > -Zeke >> > >> > On 11/12/2014 01:29 PM, Gunjan Gautam wrote: >> > > Sir earlier I was trying to use FreeSurfer using Virtual >> Box in my >> > > Windows machine. There the mri_convert command did not >> work so I >> > > switched to a Linux machine. Now, I'm using >> centos6_x86_64 version as my >> > > machine has the Ubuntu 12.04 platform and here also >> facing the same >> > > problem. >> > > >> > > I want to share one thing that in my institute I tried >> hard to download >> > > FreeSurfer but every time it resulted into a time-out >> situation so I had >> > > to ask someone to get it downloaded and send me through >> Google drive. >> > > This was how I installed it in my system. >> > > >> > > Best regards, >> > > Gunjan >> > > >> > > On Nov 12, 2014 9:15 PM, "Z K" >> > <mailto:zkauf...@nmr.mgh.harvard.edu> >> > > <mailto:zkauf...@nmr.mgh.harvard.edu >> <mailto:zkauf...@nmr.mgh.harvard.edu>>> >> > wrote: >>
Re: [Freesurfer] Regarding mri_convert command
Ok, I try this tomorrow morning. I will be thankful if you could tell me about getting brain mask and performing skull stripping otherwise I'll have to wait for 12 hours to get your replies as our working hours doesn't match. On Nov 18, 2014 8:45 PM, "Z K" wrote: > Gunjan, this may be related to an Ubuntu specific issue we address on > the Freesurfer download page: > > https://surfer.nmr.mgh.harvard.edu/fswiki/Download > > Specifically the part thats states the following: > > *** > On Ubuntu, you might have to do this if qdec or freeview complain about > libjpeg or libtiff: > > cd /usr/lib (/usr/lib/i386 or /usr/lib/x86_64 on some Ubuntu distros) > sudo ln -s libjpeg.so.8 libjpeg.so.62 > sudo ln -s libtiff.so.4 libtiff.so.3 > *** > > -Zeke > > > > > On 11/18/2014 03:55 AM, Gunjan Gautam wrote: > > Hello Sir, > > > > I have place the "license.txt" in the same directory that contains > > build-stamp.txt as there were no directory with name "FREESURFER_HOME". > > freeview command is not working and showing below message > > "freeview.bin: error while loading shared libraries: libjpeg.so.62: > > cannot open shared object file: No such file or directory". > > What next I need to do in order to generate a output brain mask. > > > > Best Regards, > > Gunjan > > > > > > > > On Thu, Nov 13, 2014 at 12:24 AM, Z K > <mailto:zkauf...@nmr.mgh.harvard.edu>> wrote: > > > > Im having a little difficulty following all the avenues of your > attempts > > to get this working, but the bottom line is that the error message > below > > is complaining that you do not have a valid license file. > > > > You need to go to this page and register and get the valid license > file: > > > > https://surfer.nmr.mgh.harvard.edu/registration.html > > > > Once you get a valid license file you will need to place it in your > > $FREESURFER_HOME directory (the same directory that contains > > build-stamp.txt) and give it the name .license or license.txt. Try > both. > > > > -Zeke > > > > On 11/12/2014 01:29 PM, Gunjan Gautam wrote: > > > Sir earlier I was trying to use FreeSurfer using Virtual Box in my > > > Windows machine. There the mri_convert command did not work so I > > > switched to a Linux machine. Now, I'm using centos6_x86_64 version > as my > > > machine has the Ubuntu 12.04 platform and here also facing the same > > > problem. > > > > > > I want to share one thing that in my institute I tried hard to > download > > > FreeSurfer but every time it resulted into a time-out situation so > I had > > > to ask someone to get it downloaded and send me through Google > drive. > > > This was how I installed it in my system. > > > > > > Best regards, > > > Gunjan > > > > > > On Nov 12, 2014 9:15 PM, "Z K" <mailto:zkauf...@nmr.mgh.harvard.edu> > > > <mailto:zkauf...@nmr.mgh.harvard.edu zkauf...@nmr.mgh.harvard.edu>>> > > wrote: > > > > > > Gunjan, > > > > > > Are you using your own version of VirtualBox, with freesurfer > installed > > > on it by you? Or the VirtualBox version of freesurfer made by > us and > > > downloaded from our website? I am confused because in your > email below, > > > freesurfer appears to be installed on the Desktop whereas the > > > prepackaged version made by us is installed in /usr/local > > > > > > -Zeke > > > > > > On 11/12/2014 08:54 AM, Gunjan Gautam wrote: > > > > Hello Sir, > > > > > > > > License file is present in the folder but with the name > LICENSE. > > > Should > > > > I download it again ? > > > > > > > > Best Regards, > > > > Gunjan > > > > > > > > On Nov 12, 2014 7:01 PM, "Bruce Fischl" > > > mailto:fis...@nmr.mgh.harvard.edu > > > > <mailto:fis...@nmr.mgh.harvard.edu fis...@nmr.mgh.harvard.edu>> > > > > <mailto:fis...@nmr.mgh.harvard.edu > > <mailto:fis...@nmr.mgh.harvard.edu> > > > <mailto:fis...@nmr.mgh.harvard.e
Re: [Freesurfer] Regarding mri_convert command
I followed the installation process from http://freesurfer.net/fswiki/LinuxInstall. while running "setenv FREESURFER_HOME /usr/local/freesurfer" it shows that setenv command not found. Is it necessary to place FreeSurfer directory in to /usr/local ? I have it on my desktop. On Tue, Nov 18, 2014 at 6:47 PM, Bruce Fischl wrote: > I think if the file existed you would have gotten a syntax error. Does it > exist? If not, then either you didn't install FreeSurfer there or something > went wrong with your installation > > > cheers > Bruce > > On Tue, 18 Nov 2014, Gunjan Gautam wrote: > > I ran but its showing error like below: >> >> bibl04@BIBL04:~/Desktop/freesurfer$ source >> /Desktop/freesurfer/SetUpFreeSurfer.csh >> bash: /Desktop/freesurfer/SetUpFreeSurfer.csh: No such file or directory >> >> >> May be due to the shell. What should I do now? >> >> >> On Tue, Nov 18, 2014 at 6:37 PM, Bruce Fischl > > >> wrote: >> Hi Gunjan >> >> FREESURFER_HOME should be an environment variable, not the name >> of a directory. It should point to the directory that you >> installed FreeSurfer in. You should run: >> >> source /SetUpFreeSurfer.csh >> >> before trying to run anything >> >> cheers >> Bruce >> >> >> On Tue, 18 Nov 2014, Gunjan Gautam wrote: >> >> Hello Sir, >> >> I have place the "license.txt" in the same directory >> that contains >> build-stamp.txt as there were no directory with name >> "FREESURFER_HOME". >> freeview command is not working and showing below >> message >> "freeview.bin: error while loading shared libraries: >> libjpeg.so.62: cannot >> open shared object file: No such file or directory". >> What next I need to do in order to generate a output >> brain mask. >> >> Best Regards, >> Gunjan >> >> >> >> On Thu, Nov 13, 2014 at 12:24 AM, Z K >> wrote: >> Im having a little difficulty following all >> the avenues of your >> attempts >> to get this working, but the bottom line is >> that the error >> message below >> is complaining that you do not have a valid >> license file. >> >> You need to go to this page and register and >> get the valid >> license file: >> >> >> https://surfer.nmr.mgh.harvard.edu/registration.html >> >> Once you get a valid license file you will >> need to place it in >> your >> $FREESURFER_HOME directory (the same directory >> that contains >> build-stamp.txt) and give it the name .license >> or license.txt. >> Try both. >> >> -Zeke >> >> On 11/12/2014 01:29 PM, Gunjan Gautam wrote: >> > Sir earlier I was trying to use FreeSurfer >> using Virtual Box >> in my >> > Windows machine. There the mri_convert >> command did not work so >> I >> > switched to a Linux machine. Now, I'm using >> centos6_x86_64 >> version as my >> > machine has the Ubuntu 12.04 platform and >> here also facing the >> same >> > problem. >> > >> > I want to share one thing that in my >> institute I tried hard to >> download >> > FreeSurfer but every time it resulted into a >> time-out >> situation so I had >> > to ask someone to get it downloaded and send >> me through Google >> drive. >> > This was how I installed it in my system. >> > >> > Best regards, >> > Gunjan >> > >> > On Nov 12, 2014 9:1
Re: [Freesurfer] Regarding mri_convert command
I ran but its showing error like below: bibl04@BIBL04:~/Desktop/freesurfer$ source /Desktop/freesurfer/SetUpFreeSurfer.csh bash: /Desktop/freesurfer/SetUpFreeSurfer.csh: No such file or directory May be due to the shell. What should I do now? On Tue, Nov 18, 2014 at 6:37 PM, Bruce Fischl wrote: > Hi Gunjan > > FREESURFER_HOME should be an environment variable, not the name of a > directory. It should point to the directory that you installed FreeSurfer > in. You should run: > > source /SetUpFreeSurfer.csh > > before trying to run anything > > cheers > Bruce > > > > On Tue, 18 Nov 2014, Gunjan Gautam wrote: > > Hello Sir, >> >> I have place the "license.txt" in the same directory that contains >> build-stamp.txt as there were no directory with name "FREESURFER_HOME". >> freeview command is not working and showing below message >> "freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot >> open shared object file: No such file or directory". >> What next I need to do in order to generate a output brain mask. >> >> Best Regards, >> Gunjan >> >> >> >> On Thu, Nov 13, 2014 at 12:24 AM, Z K >> wrote: >> Im having a little difficulty following all the avenues of your >> attempts >> to get this working, but the bottom line is that the error >> message below >> is complaining that you do not have a valid license file. >> >> You need to go to this page and register and get the valid >> license file: >> >> https://surfer.nmr.mgh.harvard.edu/registration.html >> >> Once you get a valid license file you will need to place it in >> your >> $FREESURFER_HOME directory (the same directory that contains >> build-stamp.txt) and give it the name .license or license.txt. >> Try both. >> >> -Zeke >> >> On 11/12/2014 01:29 PM, Gunjan Gautam wrote: >> > Sir earlier I was trying to use FreeSurfer using Virtual Box >> in my >> > Windows machine. There the mri_convert command did not work so >> I >> > switched to a Linux machine. Now, I'm using centos6_x86_64 >> version as my >> > machine has the Ubuntu 12.04 platform and here also facing the >> same >> > problem. >> > >> > I want to share one thing that in my institute I tried hard to >> download >> > FreeSurfer but every time it resulted into a time-out >> situation so I had >> > to ask someone to get it downloaded and send me through Google >> drive. >> > This was how I installed it in my system. >> > >> > Best regards, >> > Gunjan >> > >> > On Nov 12, 2014 9:15 PM, "Z K" > > <mailto:zkauf...@nmr.mgh.harvard.edu>> wrote: >> > >> > Gunjan, >> > >> > Are you using your own version of VirtualBox, with >> freesurfer installed >> > on it by you? Or the VirtualBox version of freesurfer made >> by us and >> > downloaded from our website? I am confused because in your >> email below, >> > freesurfer appears to be installed on the Desktop whereas >> the >> > prepackaged version made by us is installed in /usr/local >> > >> > -Zeke >> > >> > On 11/12/2014 08:54 AM, Gunjan Gautam wrote: >> > > Hello Sir, >> > > >> > > License file is present in the folder but with the name >> LICENSE. >> > Should >> > > I download it again ? >> > > >> > > Best Regards, >> > > Gunjan >> > > >> > > On Nov 12, 2014 7:01 PM, "Bruce Fischl" >> > > <mailto:fis...@nmr.mgh.harvard.edu> >> > > <mailto:fis...@nmr.mgh.harvard.edu >> > <mailto:fis...@nmr.mgh.harvard.edu>>> wrote: >> > > >> > > Hi Gunjan >> > > >> > > do you have a license? If not you need to download >> and install it >> > > (as noted in the error messag
Re: [Freesurfer] Regarding mri_convert command
Hello Sir, I have place the "license.txt" in the same directory that contains build-stamp.txt as there were no directory with name "FREESURFER_HOME". freeview command is not working and showing below message "freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory". What next I need to do in order to generate a output brain mask. Best Regards, Gunjan On Thu, Nov 13, 2014 at 12:24 AM, Z K wrote: > Im having a little difficulty following all the avenues of your attempts > to get this working, but the bottom line is that the error message below > is complaining that you do not have a valid license file. > > You need to go to this page and register and get the valid license file: > > https://surfer.nmr.mgh.harvard.edu/registration.html > > Once you get a valid license file you will need to place it in your > $FREESURFER_HOME directory (the same directory that contains > build-stamp.txt) and give it the name .license or license.txt. Try both. > > -Zeke > > On 11/12/2014 01:29 PM, Gunjan Gautam wrote: > > Sir earlier I was trying to use FreeSurfer using Virtual Box in my > > Windows machine. There the mri_convert command did not work so I > > switched to a Linux machine. Now, I'm using centos6_x86_64 version as my > > machine has the Ubuntu 12.04 platform and here also facing the same > > problem. > > > > I want to share one thing that in my institute I tried hard to download > > FreeSurfer but every time it resulted into a time-out situation so I had > > to ask someone to get it downloaded and send me through Google drive. > > This was how I installed it in my system. > > > > Best regards, > > Gunjan > > > > On Nov 12, 2014 9:15 PM, "Z K" > <mailto:zkauf...@nmr.mgh.harvard.edu>> wrote: > > > > Gunjan, > > > > Are you using your own version of VirtualBox, with freesurfer > installed > > on it by you? Or the VirtualBox version of freesurfer made by us and > > downloaded from our website? I am confused because in your email > below, > > freesurfer appears to be installed on the Desktop whereas the > > prepackaged version made by us is installed in /usr/local > > > > -Zeke > > > > On 11/12/2014 08:54 AM, Gunjan Gautam wrote: > > > Hello Sir, > > > > > > License file is present in the folder but with the name LICENSE. > > Should > > > I download it again ? > > > > > > Best Regards, > > > Gunjan > > > > > > On Nov 12, 2014 7:01 PM, "Bruce Fischl" > > mailto:fis...@nmr.mgh.harvard.edu> > > > <mailto:fis...@nmr.mgh.harvard.edu > > <mailto:fis...@nmr.mgh.harvard.edu>>> wrote: > > > > > > Hi Gunjan > > > > > > do you have a license? If not you need to download and > install it > > > (as noted in the error message). They are free. > > > > > > cheers > > > Bruce > > > On Wed, 12 Nov 2014, Gunjan Gautam wrote: > > > > > > > > > Hello Sir, > > > > > > I'm using FreeSurfer through Virtual Box. I tried the > below > > > command for > > > reslicing my volume according to a reference volume but > the > > > process gets > > > stuck at " reading volume". > > > > > > mri_convert A.nii.gz A.resliced.nii.gz -rl B.nii.gz > > > > > > A: Volume to be resampled / resliced > > > B: Reference Volume > > > > > > Error message is being shown like below: > > > > > > mri_convert a.nii a.resliced.nii -rl b.nii > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 > > mreuter Exp $ > > > reading from a.nii... > > > > > > > --__--__-- > > > ERROR: Invalid FreeSurfer license key found in license > file > > > /home/bibl04/Data_Home/__Desktop/freesurfer/license.txt > > >If you are outside the NMR-Martinos Center, > > >go to http://surfer.nmr.mgh.harvard.__edu > > > <http://surfer.nmr.mgh.harvar
Re: [Freesurfer] Regarding mri_convert command
Sir earlier I was trying to use FreeSurfer using Virtual Box in my Windows machine. There the mri_convert command did not work so I switched to a Linux machine. Now, I'm using centos6_x86_64 version as my machine has the Ubuntu 12.04 platform and here also facing the same problem. I want to share one thing that in my institute I tried hard to download FreeSurfer but every time it resulted into a time-out situation so I had to ask someone to get it downloaded and send me through Google drive. This was how I installed it in my system. Best regards, Gunjan On Nov 12, 2014 9:15 PM, "Z K" wrote: > Gunjan, > > Are you using your own version of VirtualBox, with freesurfer installed > on it by you? Or the VirtualBox version of freesurfer made by us and > downloaded from our website? I am confused because in your email below, > freesurfer appears to be installed on the Desktop whereas the > prepackaged version made by us is installed in /usr/local > > -Zeke > > On 11/12/2014 08:54 AM, Gunjan Gautam wrote: > > Hello Sir, > > > > License file is present in the folder but with the name LICENSE. Should > > I download it again ? > > > > Best Regards, > > Gunjan > > > > On Nov 12, 2014 7:01 PM, "Bruce Fischl" > <mailto:fis...@nmr.mgh.harvard.edu>> wrote: > > > > Hi Gunjan > > > > do you have a license? If not you need to download and install it > > (as noted in the error message). They are free. > > > > cheers > > Bruce > > On Wed, 12 Nov 2014, Gunjan Gautam wrote: > > > > > > Hello Sir, > > > > I'm using FreeSurfer through Virtual Box. I tried the below > > command for > > reslicing my volume according to a reference volume but the > > process gets > > stuck at " reading volume". > > > > mri_convert A.nii.gz A.resliced.nii.gz -rl B.nii.gz > > > > A: Volume to be resampled / resliced > > B: Reference Volume > > > > Error message is being shown like below: > > > > mri_convert a.nii a.resliced.nii -rl b.nii > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from a.nii... > > > > --__--__-- > > ERROR: Invalid FreeSurfer license key found in license file > > /home/bibl04/Data_Home/__Desktop/freesurfer/license.txt > >If you are outside the NMR-Martinos Center, > >go to http://surfer.nmr.mgh.harvard.__edu > > <http://surfer.nmr.mgh.harvard.edu> to > >get a valid license file (it's free). > >If you are inside the NMR-Martinos Center, > >make sure to source the standard environment. > > > > Actually, I have two volumes, belong to the same subject. One > > volume is the > > ground truth which will be considered as standard for the second > > volume > > which is the processed one or the extracted brain. To perform a > > perfect > > comparison between both volumes, these must generate equal > > number of slices > > in order to compare the corresponding slide. But here there is > > problem with > > my volumes, that is while performing slicing Ground Truth volume > is > > generating 360 slice and processed volume is generating 181 > > slides. So > > comparison can't take place in this way. > > > > What all I need is to do the resampling or generating the 181 > > slides from > > the Ground Truth as well. > > > > > > Best Regards, > > Gunjan > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu 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 . If the e-mail was sent to > > you in error > > but does not contain patient information, please contact the sender > >
Re: [Freesurfer] Regarding mri_convert command
Hello Sir, License file is present in the folder but with the name LICENSE. Should I download it again ? Best Regards, Gunjan On Nov 12, 2014 7:01 PM, "Bruce Fischl" wrote: > Hi Gunjan > > do you have a license? If not you need to download and install it (as > noted in the error message). They are free. > > cheers > Bruce > On Wed, 12 Nov 2014, Gunjan Gautam wrote: > > >> Hello Sir, >> >> I'm using FreeSurfer through Virtual Box. I tried the below command for >> reslicing my volume according to a reference volume but the process gets >> stuck at " reading volume". >> >> mri_convert A.nii.gz A.resliced.nii.gz -rl B.nii.gz >> >> A: Volume to be resampled / resliced >> B: Reference Volume >> >> Error message is being shown like below: >> >> mri_convert a.nii a.resliced.nii -rl b.nii >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from a.nii... >> >> -- >> ERROR: Invalid FreeSurfer license key found in license file >> /home/bibl04/Data_Home/Desktop/freesurfer/license.txt >> If you are outside the NMR-Martinos Center, >> go to http://surfer.nmr.mgh.harvard.edu to >> get a valid license file (it's free). >> If you are inside the NMR-Martinos Center, >> make sure to source the standard environment. >> >> Actually, I have two volumes, belong to the same subject. One volume is >> the >> ground truth which will be considered as standard for the second volume >> which is the processed one or the extracted brain. To perform a perfect >> comparison between both volumes, these must generate equal number of >> slices >> in order to compare the corresponding slide. But here there is problem >> with >> my volumes, that is while performing slicing Ground Truth volume is >> generating 360 slice and processed volume is generating 181 slides. So >> comparison can't take place in this way. >> >> What all I need is to do the resampling or generating the 181 slides from >> the Ground Truth as well. >> >> >> Best Regards, >> Gunjan >> >> >> > ___ > 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 . 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. > > ___ 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 . 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.
[Freesurfer] Regarding mri_convert command
Hello Sir, I'm using FreeSurfer through Virtual Box. I tried the below command for reslicing my volume according to a reference volume but the process gets stuck at " reading volume". *mri_convert A.nii.gz A.resliced.nii.gz -rl B.nii.gz* A: Volume to be resampled / resliced B: Reference Volume Error message is being shown like below: mri_convert a.nii a.resliced.nii -rl b.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from a.nii... -- ERROR: Invalid FreeSurfer license key found in license file /home/bibl04/Data_Home/Desktop/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. Actually, I have two volumes, belong to the same subject. One volume is the ground truth which will be considered as standard for the second volume which is the processed one or the extracted brain. To perform a perfect comparison between both volumes, these must generate equal number of slices in order to compare the corresponding slide. But here there is problem with my volumes, that is while performing slicing Ground Truth volume is generating 360 slice and processed volume is generating 181 slides. So comparison can't take place in this way. What all I need is to do the resampling or generating the 181 slides from the Ground Truth as well. Best Regards, Gunjan ___ 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 . 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.
