Dear FreeSurfers,
The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, L3,..) in nifti format. On this data I would like to start tracula starting from step 1.3.
I have organized the data as mentioned on the wiki: For example: <subjID>/<dmri> dtifit_FA.nii.gz
I have also filled in the configuration file, canceling out the things I don't need and then I tried to run: Trac-all -intra -c <configuration file>
Unfortunately, it does not work, it says: dcmlist: subscript out of range
I do not have the original files... is there a way that I can get the script working?
Many thanks. Heidi
Hi Heidi - The intra-subject registration step that you're trying to run registers your subject's DWI and T1 images. It expects to find those images. It doesn't use the FA, MD, etc in any way.
Did the log file get created in scripts/trac-all.log? If so, can you please send that file and your configuration file? Thanks!
a.y
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Dear FreeSurfers,
The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, L3,..) in nifti format. On this data I would like to start tracula starting from step 1.3.
I have organized the data as mentioned on the wiki: For example: <subjID>/<dmri> dtifit_FA.nii.gz
I have also filled in the configuration file, canceling out the things I don’t need and then I tried to run: Trac-all –intra –c <configuration file>
Unfortunately, it does not work, it says: dcmlist: subscript out of range
I do not have the original files… is there a way that I can get the script working?
Many thanks. Heidi
Dear Anastasia,
Thanks for the feedback. So, does this mean that the dcm root should be pointed towards the T1¹s? I have the FreeSurfer recon-all output in a different folder. Enclosed is the log file (of one subject) and the configuration file. You will see that I tried the inter and intra option, because I thought that for the inter it would not need anything else than the MNI template and the DTI images.
Thanks
Best Heidi
On 5/31/16, 4:01 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Heidi - The intra-subject registration step that you're trying to run registers your subject's DWI and T1 images. It expects to find those images. It doesn't use the FA, MD, etc in any way.
Did the log file get created in scripts/trac-all.log? If so, can you please send that file and your configuration file? Thanks!
a.y
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Dear FreeSurfers,
The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, L3,..) in nifti format. On this data I would like to start tracula starting from step 1.3.
I have organized the data as mentioned on the wiki: For example: <subjID>/<dmri> dtifit_FA.nii.gz
I have also filled in the configuration file, canceling out the things I don¹t need and then I tried to run: Trac-all intra c <configuration file>
Unfortunately, it does not work, it says: dcmlist: subscript out of range
I do not have the original filesŠ is there a way that I can get the script working?
Many thanks. Heidi
No, it should be pointed to the DWI data, which can be corrected niftis instead of the original dicoms. I would recommend turning off all the corrections in the configuration file, and then running everything without skipping steps. This will create all the files that are expected to be there for the registration.
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Dear Anastasia,
Thanks for the feedback. So, does this mean that the dcm root should be pointed towards the T1¹s? I have the FreeSurfer recon-all output in a different folder. Enclosed is the log file (of one subject) and the configuration file. You will see that I tried the inter and intra option, because I thought that for the inter it would not need anything else than the MNI template and the DTI images.
Thanks
Best Heidi
On 5/31/16, 4:01 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Heidi - The intra-subject registration step that you're trying to run registers your subject's DWI and T1 images. It expects to find those images. It doesn't use the FA, MD, etc in any way.
Did the log file get created in scripts/trac-all.log? If so, can you please send that file and your configuration file? Thanks!
a.y
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Dear FreeSurfers,
The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, L3,..) in nifti format. On this data I would like to start tracula starting from step 1.3.
I have organized the data as mentioned on the wiki: For example: <subjID>/<dmri> dtifit_FA.nii.gz
I have also filled in the configuration file, canceling out the things I don¹t need and then I tried to run: Trac-all intra c <configuration file>
Unfortunately, it does not work, it says: dcmlist: subscript out of range
I do not have the original filesŠ is there a way that I can get the script working?
Many thanks. Heidi
Thanks! I tried to adapt the configuration file and it got a bit further, but then crashes again. Not sure why? I have added the log file, so that maybe you could have a look at what is happening? Also, how does the trac-all command knows where to find the T1 data? Thanks Heidi
On 5/31/16, 5:07 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
No, it should be pointed to the DWI data, which can be corrected niftis instead of the original dicoms. I would recommend turning off all the corrections in the configuration file, and then running everything without skipping steps. This will create all the files that are expected to be there for the registration.
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Dear Anastasia,
Thanks for the feedback. So, does this mean that the dcm root should be pointed towards the T1¹s? I have the FreeSurfer recon-all output in a different folder. Enclosed is the log file (of one subject) and the configuration file. You will see that I tried the inter and intra option, because I thought that for the inter it would not need anything else than the MNI template and the DTI images.
Thanks
Best Heidi
On 5/31/16, 4:01 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Heidi - The intra-subject registration step that you're trying to run registers your subject's DWI and T1 images. It expects to find those images. It doesn't use the FA, MD, etc in any way.
Did the log file get created in scripts/trac-all.log? If so, can you please send that file and your configuration file? Thanks!
a.y
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Dear FreeSurfers,
The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, L3,..) in nifti format. On this data I would like to start tracula starting from step 1.3.
I have organized the data as mentioned on the wiki: For example: <subjID>/<dmri> dtifit_FA.nii.gz
I have also filled in the configuration file, canceling out the things I don¹t need and then I tried to run: Trac-all intra c <configuration file>
Unfortunately, it does not work, it says: dcmlist: subscript out of range
I do not have the original filesŠ is there a way that I can get the script working?
Many thanks. Heidi
Hi Heidi - It knows where to find the freesurfer recons of the T1's from SUBJECTS_DIR (see example config file). Based on your log file, it looks like you haven't turned off the eddy current compensation, because it's trying to run it. If you attach your config file, I'll take a look.
Best, a.y
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Thanks! I tried to adapt the configuration file and it got a bit further, but then crashes again. Not sure why? I have added the log file, so that maybe you could have a look at what is happening? Also, how does the trac-all command knows where to find the T1 data? Thanks Heidi
On 5/31/16, 5:07 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
No, it should be pointed to the DWI data, which can be corrected niftis instead of the original dicoms. I would recommend turning off all the corrections in the configuration file, and then running everything without skipping steps. This will create all the files that are expected to be there for the registration.
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Dear Anastasia,
Thanks for the feedback. So, does this mean that the dcm root should be pointed towards the T1¹s? I have the FreeSurfer recon-all output in a different folder. Enclosed is the log file (of one subject) and the configuration file. You will see that I tried the inter and intra option, because I thought that for the inter it would not need anything else than the MNI template and the DTI images.
Thanks
Best Heidi
On 5/31/16, 4:01 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Heidi - The intra-subject registration step that you're trying to run registers your subject's DWI and T1 images. It expects to find those images. It doesn't use the FA, MD, etc in any way.
Did the log file get created in scripts/trac-all.log? If so, can you please send that file and your configuration file? Thanks!
a.y
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Dear FreeSurfers,
The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, L3,..) in nifti format. On this data I would like to start tracula starting from step 1.3.
I have organized the data as mentioned on the wiki: For example: <subjID>/<dmri> dtifit_FA.nii.gz
I have also filled in the configuration file, canceling out the things I don¹t need and then I tried to run: Trac-all intra c <configuration file>
Unfortunately, it does not work, it says: dcmlist: subscript out of range
I do not have the original filesŠ is there a way that I can get the script working?
Many thanks. Heidi
Hmm, weird, as I put a # in front of it. Putting the eddy current to 0 gives the same error. Enclosed is the config file. Thank you so much Heidi
On 5/31/16, 8:13 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Heidi - It knows where to find the freesurfer recons of the T1's from SUBJECTS_DIR (see example config file). Based on your log file, it looks like you haven't turned off the eddy current compensation, because it's trying to run it. If you attach your config file, I'll take a look.
Best, a.y
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Thanks! I tried to adapt the configuration file and it got a bit further, but then crashes again. Not sure why? I have added the log file, so that maybe you could have a look at what is happening? Also, how does the trac-all command knows where to find the T1 data? Thanks Heidi
On 5/31/16, 5:07 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
No, it should be pointed to the DWI data, which can be corrected niftis instead of the original dicoms. I would recommend turning off all the corrections in the configuration file, and then running everything without skipping steps. This will create all the files that are expected to be there for the registration.
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Dear Anastasia,
Thanks for the feedback. So, does this mean that the dcm root should be pointed towards the T1¹s? I have the FreeSurfer recon-all output in a different folder. Enclosed is the log file (of one subject) and the configuration file. You will see that I tried the inter and intra option, because I thought that for the inter it would not need anything else than the MNI template and the DTI images.
Thanks
Best Heidi
On 5/31/16, 4:01 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Heidi - The intra-subject registration step that you're trying to run registers your subject's DWI and T1 images. It expects to find those images. It doesn't use the FA, MD, etc in any way.
Did the log file get created in scripts/trac-all.log? If so, can you please send that file and your configuration file? Thanks!
a.y
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Dear FreeSurfers,
The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, L3,..) in nifti format. On this data I would like to start tracula starting from step 1.3.
I have organized the data as mentioned on the wiki: For example: <subjID>/<dmri> dtifit_FA.nii.gz
I have also filled in the configuration file, canceling out the things I don¹t need and then I tried to run: Trac-all intra c <configuration file>
Unfortunately, it does not work, it says: dcmlist: subscript out of range
I do not have the original filesŠ is there a way that I can get the script working?
Many thanks. Heidi
Some of the errors make me suspect that your input DWI files contain only one volume. Could this be the case?
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Hmm, weird, as I put a # in front of it. Putting the eddy current to 0 gives the same error. Enclosed is the config file. Thank you so much Heidi
On 5/31/16, 8:13 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Heidi - It knows where to find the freesurfer recons of the T1's from SUBJECTS_DIR (see example config file). Based on your log file, it looks like you haven't turned off the eddy current compensation, because it's trying to run it. If you attach your config file, I'll take a look.
Best, a.y
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Thanks! I tried to adapt the configuration file and it got a bit further, but then crashes again. Not sure why? I have added the log file, so that maybe you could have a look at what is happening? Also, how does the trac-all command knows where to find the T1 data? Thanks Heidi
On 5/31/16, 5:07 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
No, it should be pointed to the DWI data, which can be corrected niftis instead of the original dicoms. I would recommend turning off all the corrections in the configuration file, and then running everything without skipping steps. This will create all the files that are expected to be there for the registration.
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Dear Anastasia,
Thanks for the feedback. So, does this mean that the dcm root should be pointed towards the T1¹s? I have the FreeSurfer recon-all output in a different folder. Enclosed is the log file (of one subject) and the configuration file. You will see that I tried the inter and intra option, because I thought that for the inter it would not need anything else than the MNI template and the DTI images.
Thanks
Best Heidi
On 5/31/16, 4:01 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Heidi - The intra-subject registration step that you're trying to run registers your subject's DWI and T1 images. It expects to find those images. It doesn't use the FA, MD, etc in any way.
Did the log file get created in scripts/trac-all.log? If so, can you please send that file and your configuration file? Thanks!
a.y
On Tue, 31 May 2016, Jacobs H (NP) wrote:
> Dear FreeSurfers, > > The data I have is preprocessed, so I have the all the metrics (FA, > MD, > L1, L2, L3,..) in nifti format. > On this data I would like to start tracula starting from step 1.3. > > I have organized the data as mentioned on the wiki: > For example: > <subjID>/<dmri> dtifit_FA.nii.gz > > I have also filled in the configuration file, canceling out the > things > I don¹t need and then I tried to run: > Trac-all intra c <configuration file> > > Unfortunately, it does not work, it says: dcmlist: subscript out of > range > > I do not have the original filesŠ is there a way that I can get the > script working? > > Many thanks. > Heidi >
Yes, each nifti contains one volume. I have different nifti’s for the different metrics (FA, MD,..) Is there a way I can use the trac-all on these files?
On 5/31/16, 9:26 PM, "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu wrote:
Some of the errors make me suspect that your input DWI files contain only one volume. Could this be the case?
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Hmm, weird, as I put a # in front of it. Putting the eddy current to 0 gives the same error. Enclosed is the config file. Thank you so much Heidi
On 5/31/16, 8:13 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Heidi - It knows where to find the freesurfer recons of the T1's from SUBJECTS_DIR (see example config file). Based on your log file, it looks like you haven't turned off the eddy current compensation, because it's trying to run it. If you attach your config file, I'll take a look.
Best, a.y
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Thanks! I tried to adapt the configuration file and it got a bit further, but then crashes again. Not sure why? I have added the log file, so that maybe you could have a look at what is happening? Also, how does the trac-all command knows where to find the T1 data? Thanks Heidi
On 5/31/16, 5:07 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
No, it should be pointed to the DWI data, which can be corrected niftis instead of the original dicoms. I would recommend turning off all the corrections in the configuration file, and then running everything without skipping steps. This will create all the files that are expected to be there for the registration.
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Dear Anastasia,
Thanks for the feedback. So, does this mean that the dcm root should be pointed towards the T1¹s? I have the FreeSurfer recon-all output in a different folder. Enclosed is the log file (of one subject) and the configuration file. You will see that I tried the inter and intra option, because I thought that for the inter it would not need anything else than the MNI template and the DTI images.
Thanks
Best Heidi
On 5/31/16, 4:01 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
> > Hi Heidi - The intra-subject registration step that you're trying >to > run > registers your subject's DWI and T1 images. It expects to find >those > images. It doesn't use the FA, MD, etc in any way. > > Did the log file get created in scripts/trac-all.log? If so, can >you > please send that file and your configuration file? Thanks! > > a.y > > On Tue, 31 May 2016, Jacobs H (NP) wrote: > >> Dear FreeSurfers, >> >> The data I have is preprocessed, so I have the all the metrics >>(FA, >> MD, >> L1, L2, L3,..) in nifti format. >> On this data I would like to start tracula starting from step 1.3. >> >> I have organized the data as mentioned on the wiki: >> For example: >> <subjID>/<dmri> dtifit_FA.nii.gz >> >> I have also filled in the configuration file, canceling out the >> things >> I don¹t need and then I tried to run: >> Trac-all intra c <configuration file> >> >> Unfortunately, it does not work, it says: dcmlist: subscript out >>of >> range >> >> I do not have the original filesŠ is there a way that I can get >>the >> script working? >> >> Many thanks. >> Heidi >>
The input needs to be the diffusion-weighted images, not the FA, MD, etc. There should be as many volumes in this input nifti as there are b-values in bval file and gradient vectors in the bvec file. The image registration, tractography, etc etc is performed on the diffusion-weighted images, not on the FA, MD, etc. The FA, MD, etc are used only in the very end, to extract FA, MD, etc for each tract. But to get the tracts in the first place, you need the images.
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Yes, each nifti contains one volume. I have different nifti’s for the different metrics (FA, MD,..) Is there a way I can use the trac-all on these files?
On 5/31/16, 9:26 PM, "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu wrote:
Some of the errors make me suspect that your input DWI files contain only one volume. Could this be the case?
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Hmm, weird, as I put a # in front of it. Putting the eddy current to 0 gives the same error. Enclosed is the config file. Thank you so much Heidi
On 5/31/16, 8:13 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Heidi - It knows where to find the freesurfer recons of the T1's from SUBJECTS_DIR (see example config file). Based on your log file, it looks like you haven't turned off the eddy current compensation, because it's trying to run it. If you attach your config file, I'll take a look.
Best, a.y
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Thanks! I tried to adapt the configuration file and it got a bit further, but then crashes again. Not sure why? I have added the log file, so that maybe you could have a look at what is happening? Also, how does the trac-all command knows where to find the T1 data? Thanks Heidi
On 5/31/16, 5:07 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
No, it should be pointed to the DWI data, which can be corrected niftis instead of the original dicoms. I would recommend turning off all the corrections in the configuration file, and then running everything without skipping steps. This will create all the files that are expected to be there for the registration.
On Tue, 31 May 2016, Jacobs H (NP) wrote:
> Dear Anastasia, > > Thanks for the feedback. So, does this mean that the dcm root should > be > pointed towards the T1¹s? I have the FreeSurfer recon-all output in > a > different folder. > Enclosed is the log file (of one subject) and the configuration > file. > You > will see that I tried the inter and intra option, because I thought > that > for the inter it would not need anything else than the MNI template > and > the DTI images. > > Thanks > > Best > Heidi > > On 5/31/16, 4:01 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on > behalf > of > Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf > of > ayendiki@nmr.mgh.harvard.edu> wrote: > >> >> Hi Heidi - The intra-subject registration step that you're trying >> to >> run >> registers your subject's DWI and T1 images. It expects to find >> those >> images. It doesn't use the FA, MD, etc in any way. >> >> Did the log file get created in scripts/trac-all.log? If so, can >> you >> please send that file and your configuration file? Thanks! >> >> a.y >> >> On Tue, 31 May 2016, Jacobs H (NP) wrote: >> >>> Dear FreeSurfers, >>> >>> The data I have is preprocessed, so I have the all the metrics >>> (FA, >>> MD, >>> L1, L2, L3,..) in nifti format. >>> On this data I would like to start tracula starting from step 1.3. >>> >>> I have organized the data as mentioned on the wiki: >>> For example: >>> <subjID>/<dmri> dtifit_FA.nii.gz >>> >>> I have also filled in the configuration file, canceling out the >>> things >>> I don¹t need and then I tried to run: >>> Trac-all intra c <configuration file> >>> >>> Unfortunately, it does not work, it says: dcmlist: subscript out >>> of >>> range >>> >>> I do not have the original filesŠ is there a way that I can get >>> the >>> script working? >>> >>> Many thanks. >>> Heidi >>> >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Aha, Ok, I will try to get my hands on that data and give it a go. Thanks for the help! Heidi
On 6/1/16, 4:01 AM, "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu wrote:
The input needs to be the diffusion-weighted images, not the FA, MD, etc. There should be as many volumes in this input nifti as there are b-values in bval file and gradient vectors in the bvec file. The image registration, tractography, etc etc is performed on the diffusion-weighted images, not on the FA, MD, etc. The FA, MD, etc are used only in the very end, to extract FA, MD, etc for each tract. But to get the tracts in the first place, you need the images.
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Yes, each nifti contains one volume. I have different nifti’s for the different metrics (FA, MD,..) Is there a way I can use the trac-all on these files?
On 5/31/16, 9:26 PM, "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu wrote:
Some of the errors make me suspect that your input DWI files contain only one volume. Could this be the case?
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Hmm, weird, as I put a # in front of it. Putting the eddy current to 0 gives the same error. Enclosed is the config file. Thank you so much Heidi
On 5/31/16, 8:13 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Heidi - It knows where to find the freesurfer recons of the T1's from SUBJECTS_DIR (see example config file). Based on your log file, it looks like you haven't turned off the eddy current compensation, because it's trying to run it. If you attach your config file, I'll take a look.
Best, a.y
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Thanks! I tried to adapt the configuration file and it got a bit further, but then crashes again. Not sure why? I have added the log file, so that maybe you could have a look at what is happening? Also, how does the trac-all command knows where to find the T1 data? Thanks Heidi
On 5/31/16, 5:07 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ayendiki@nmr.mgh.harvard.edu> wrote:
> > No, it should be pointed to the DWI data, which can be corrected > niftis > instead of the original dicoms. I would recommend turning off all >the > corrections in the configuration file, and then running everything > without > skipping steps. This will create all the files that are expected to > be > there for the registration. > > On Tue, 31 May 2016, Jacobs H (NP) wrote: > >> Dear Anastasia, >> >> Thanks for the feedback. So, does this mean that the dcm root >>should >> be >> pointed towards the T1¹s? I have the FreeSurfer recon-all output >>in >> a >> different folder. >> Enclosed is the log file (of one subject) and the configuration >> file. >> You >> will see that I tried the inter and intra option, because I >>thought >> that >> for the inter it would not need anything else than the MNI >>template >> and >> the DTI images. >> >> Thanks >> >> Best >> Heidi >> >> On 5/31/16, 4:01 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on >> behalf >> of >> Anastasia Yendiki" <freesurfer-bounces@nmr.mgh.harvard.edu on >>behalf >> of >> ayendiki@nmr.mgh.harvard.edu> wrote: >> >>> >>> Hi Heidi - The intra-subject registration step that you're trying >>> to >>> run >>> registers your subject's DWI and T1 images. It expects to find >>> those >>> images. It doesn't use the FA, MD, etc in any way. >>> >>> Did the log file get created in scripts/trac-all.log? If so, can >>> you >>> please send that file and your configuration file? Thanks! >>> >>> a.y >>> >>> On Tue, 31 May 2016, Jacobs H (NP) wrote: >>> >>>> Dear FreeSurfers, >>>> >>>> The data I have is preprocessed, so I have the all the metrics >>>> (FA, >>>> MD, >>>> L1, L2, L3,..) in nifti format. >>>> On this data I would like to start tracula starting from step >>>>1.3. >>>> >>>> I have organized the data as mentioned on the wiki: >>>> For example: >>>> <subjID>/<dmri> dtifit_FA.nii.gz >>>> >>>> I have also filled in the configuration file, canceling out the >>>> things >>>> I don¹t need and then I tried to run: >>>> Trac-all intra c <configuration file> >>>> >>>> Unfortunately, it does not work, it says: dcmlist: subscript out >>>> of >>>> range >>>> >>>> I do not have the original filesŠ is there a way that I can get >>>> the >>>> script working? >>>> >>>> Many thanks. >>>> Heidi >>>> >>
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