[Freesurfer] mri_convert
Hi, I have the data from one of our collaborators. They are dicom files, and they are collected from GE. I try to use mri_convert to convert the files from dicom to nifti. However, the following error shows up. mri_convert 1.2.840.113619.2.135.2025.3762570.5144.1309404440.95.dcm 1.2.840.113619.2.135.2025.3762570.5144.1309404440.95.nii.gz mri_convert 1.2.840.113619.2.135.2025.3762570.5144.1309404440.95.dcm 1.2.840.113619.2.135.2025.3762570.5144.1309404440.95.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from 1.2.840.113619.2.135.2025.3762570.5144.1309404440.95.dcm... Starting DICOMRead2() dcmfile = /autofs/cluster/randy/5/helen/resting_jiliang/1.2.840.113619.2.135.2025.3762570.5144.1309404440.95.dcm dcmdir = /autofs/cluster/randy/5/helen/resting_jiliang Ref Series No = 2 Found 15 files, checking for dicoms Found 1 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 0 Vs: nan nan nan Second Sorting Counting frames nframes = 1 nslices = 1 ndcmfiles = 1 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=2500.00, TE=30.00, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -0.974123, -0.226021) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is nan, matrix is: -3.750 0.000 nan nan; 0.000 -3.653 nan nan; 0.000 -0.848 nan nan; 0.000 0.000 0.000 1.000; Please suggest the possible reason for the error. Thanks a lot! Helen On Jul 3, 2012, at 11:55 AM, Bruce Fischl wrote: > Hi Brianna > > If the white surface is correct and you can't get watershed/graph cuts to do > any better, it may be that erasing voxels from the brainmask or > brain.finalsurfs is your only option. If you had multi-echo MPRAGE you might > be able to get rid of it also. > > sorry, > Bruce > On Tue, 3 Jul 2012, Kolody, Brianna wrote: > >> Hi, >> We are having problems with some of our pial surfaces extending into the >> sagittal sinus. We are interested in cortical thickness around the >> precuneus, etc. I attached a couple screen shots to describe. The error is >> not repaired by adjusting watershed parameters. How do you suggest we >> proceed? Should we erase voxels from brainmask? We are concerned since these >> errors extend for a significant number of slices, in many subjects, and >> include such a large amount of the sinus. >> As a second part to this question, I am unclear on how cortical thickness is >> calculated and whether the statistics are directly derived from the visible >> surfaces. For instance, when there is an error with the cortical surface >> image including the sagittal sinus, it also visibly appears as an error in >> aseg and aparc. However, the mistaken area doesn't have an associated region >> label in aseg or aparc when we move the cursor over it. Are the cortical >> thickness statistics reflected by the parcellation, which possibly does not >> include the sinus, or the surfaces, which do seem to include the sinus? >> Brianna >> >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return 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] flip brain
Dear Freesurfer experts, I have a general question regarding data analysis. Our group has collected data from patients with OA, some of them received treatment on their left leg, some of them on their right leg. We would like to flip the brain for the people that received treatment on their left leg to match the right leg group. Next, we would like perform group analysis on them. My question is, when should we flip the brain for the left leg group patients? Should we flip the raw images before we do any preprocessing at the individual level? Or should we flip the first level contrast images when we get some results for each of these subjects? I tried to flip the contrast images, but it seems to give me a lot of error at the second level group analysis level. It says that the flipped contrast image does not match the unflipped contrast image in orientation. Thank you very much. Helen ___ 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] bbregister with SPM
Dear freesurfer experts, I have a question regarding how to incorporating bbregister coregistered mean image into the SPM batch. After realignment step, I convert the mean functional image from the analyze format to nii format (to avoid flipping brain using bbregister) Then, I use bbregister to co-register the mean functional image to subjects' surfaces using following command bbregister -- s subject_name_freesurfer -- mov mean.nii --init-spm -- bold --reg register.dat -- spm-nii After this step, is the mean.nii the coregistered image already? If it is, in SPM, shall I skip the coregistration and segmentation step? If I do skip them, in the Normalization step, is the following correct? source image: mean.nii that has been coregistered in bbregister image to write: (Dependency) realigned session1 and realigned session2 template image: EPI Thank you very much for your help. Helen ___ 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] bbregister with SPM
Doug, Do you mean that the functional file mean.nii is not aligned with the structural data? I know that -- o means resample mov and save as outvol. Why do you need to resample the mean.nii? To align with structural data in freesurfer? If you do that, will the outvol be able to later be incorporated into SPM since it's not in the same dimension as it originally was? Thank you very much. I added -- spm-nii previously. Does this works? >> bbregister -- s subject_name_freesurfer -- mov mean.nii --init-spm -- bold >> --reg register.dat -- spm-nii -- o mean_new.nii Helen On Feb 28, 2013, at 6:29 PM, Douglas N Greve wrote: > > Hi Helen, it is not aligned. You will need to apply the registration > with mri_vol2vol or use the --o option to output a volume. I did not > follow how you are trying to incorporate this into the SPM pipeline. > Also note that if you are using SPM8, make sure to added --spm-nii or > else you will get LR reversals. > doug > > On 02/28/2013 04:24 PM, Chen, Xiaoyan wrote: >> Dear freesurfer experts, >> I have a question regarding how to >> incorporating bbregister coregistered mean image into the SPM batch. >> >> After realignment step, I convert the mean functional image from the analyze >> format to nii format (to avoid flipping brain using bbregister) >> >> Then, I use bbregister to co-register the mean functional image to subjects' >> surfaces using following command >> >> >> bbregister -- s subject_name_freesurfer -- mov mean.nii --init-spm -- bold >> --reg register.dat -- spm-nii >> >> >> After this step, is the mean.nii the coregistered image already? If it is, >> in SPM, shall I skip the coregistration and segmentation step? If I do skip >> them, in the Normalization step, is the following correct? >> >> source image: mean.nii that has been coregistered in bbregister >> >> image to write: (Dependency) realigned session1 and realigned session2 >> >> template image: EPI >> >> >> Thank you very much for your help. >> >> >> >> Helen >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > 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] set path for BBR
Hi, If I want to use epi_reg, what do I need to do for the environment in fsl? It says that it's not recognizing the function bbr. How do find the path to BBR in /usr/pubsw? Thank you very much. Helen ___ 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] set path for BBR
Doug,
epi_reg is using BBregister with FSL. In FSL5 they incorporated
the tool your guys developed. The following is the error message
[mi2b2:OAEAA005] (nmr-stable5.1-env) epi_reg --epi=meanuf-ep2d-18-0001.nii.gz
--t1=MPRAGE1.nii.gz --t1brain=MPRAGE1_manual2.nii.gz --out=epi2struct.nii.gz
Running FAST segmentation
FLIRT pre-alignment
Running BBR
Unrecognised cost function type: bbr
Could not open matrix file epi2struct.mat
terminate called after throwing an instance of
'NEWMAT::IncompatibleDimensionsException'
/usr/pubsw/packages/fsl/5.0.1/bin/epi_reg: line 353: 47296 Aborted
(core dumped) $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o ${vout}
--premat=${vout}.mat --interp=spline
[mi2b2:OAEAA005] (nmr-stable5.1-env) epi_reg --epi=meanuf-ep2d-18-0001.nii.gz
--t1=MPRAGE1.nii.gz --t1brain=MPRAGE1_manual2.nii.gz --out=epi2struct
Running FAST segmentation
FLIRT pre-alignment
Running BBR
Unrecognised cost function type: bbr
Could not open matrix file epi2struct.mat
terminate called after throwing an instance of
'NEWMAT::IncompatibleDimensionsException'
/usr/pubsw/packages/fsl/5.0.1/bin/epi_reg: line 353: 48263 Aborted
(core dumped) $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o ${vout}
--premat=${vout}.mat --interp=spline
Helen
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, March 01, 2013 2:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] set path for BBR
what is epi_reg? Is that an FS program?
On 03/01/2013 02:19 PM, Chen, Xiaoyan wrote:
> Hi,
>
> If I want to use epi_reg, what do I need to do for the environment in fsl? It
> says that it's not recognizing the function bbr. How do find the path to BBR
> in /usr/pubsw?
>
> Thank you very much.
>
> Helen
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
___
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.
Re: [Freesurfer] set path for BBR
Dear all,
Thank you so much! It works now.
Helen
On Mar 1, 2013, at 2:41 PM, Mark Jenkinson wrote:
> Hi,
>
> It looks like your installation isn't right - you need FSL5.0 or higher for
> this to work. If not I would expect it to complain about: "Unrecognised cost
> function type: bbr" as it seems to do.
>
> Maybe you should check that you are picking up the right version of FSL, by
> doing:
> which flirt
> and
> echo $FSLDIR
>
> Only if these are both pointing at the same place and are installations of
> FSL5.0 or higher, would this work.
>
> All the best,
> Mark
>
>
>
>
> On 1 Mar 2013, at 19:31, Bruce Fischl
> wrote:
>
>> oh, this is the FSL reimplementation of Doug's algorithm (they loved it so
>> much they had to have their own!). You'll need to ask them about it. I'll cc
>> MJ so he can chime in.
>>
>> cheers
>> Bruce
>>
>>
>>
>>
>> On Fri, 1 Mar 2013, Chen, Xiaoyan wrote:
>>
>>> Doug,
>>> epi_reg is using BBregister with FSL. In FSL5 they incorporated
>>> the tool your guys developed. The following is the error message
>>>
>>> [mi2b2:OAEAA005] (nmr-stable5.1-env) epi_reg
>>> --epi=meanuf-ep2d-18-0001.nii.gz --t1=MPRAGE1.nii.gz
>>> --t1brain=MPRAGE1_manual2.nii.gz --out=epi2struct.nii.gz
>>> Running FAST segmentation
>>> FLIRT pre-alignment
>>> Running BBR
>>> Unrecognised cost function type: bbr
>>> Could not open matrix file epi2struct.mat
>>> terminate called after throwing an instance of
>>> 'NEWMAT::IncompatibleDimensionsException'
>>> /usr/pubsw/packages/fsl/5.0.1/bin/epi_reg: line 353: 47296 Aborted
>>>(core dumped) $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o
>>> ${vout} --premat=${vout}.mat --interp=spline
>>> [mi2b2:OAEAA005] (nmr-stable5.1-env) epi_reg
>>> --epi=meanuf-ep2d-18-0001.nii.gz --t1=MPRAGE1.nii.gz
>>> --t1brain=MPRAGE1_manual2.nii.gz --out=epi2struct
>>> Running FAST segmentation
>>> FLIRT pre-alignment
>>> Running BBR
>>> Unrecognised cost function type: bbr
>>> Could not open matrix file epi2struct.mat
>>> terminate called after throwing an instance of
>>> 'NEWMAT::IncompatibleDimensionsException'
>>> /usr/pubsw/packages/fsl/5.0.1/bin/epi_reg: line 353: 48263 Aborted
>>>(core dumped) $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o
>>> ${vout} --premat=${vout}.mat --interp=spline
>>>
>>>
>>>
>>> Helen
>>>
>>>
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Friday, March 01, 2013 2:22 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] set path for BBR
>>>
>>> what is epi_reg? Is that an FS program?
>>>
>>> On 03/01/2013 02:19 PM, Chen, Xiaoyan wrote:
>>>> Hi,
>>>>
>>>> If I want to use epi_reg, what do I need to do for the environment in fsl?
>>>> It says that it's not recognizing the function bbr. How do find the path
>>>> to BBR in /usr/pubsw?
>>>>
>>>> Thank you very much.
>>>>
>>>> Helen
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
>>> ___
>>> 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.
>>
>>
>
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