Hi Colm - Yes, it's fine to run bedpostx directly, with the path to the dmri directory as its argument.

Since you're using 5.2, note that although there were no issues with tracula in that version, it is not advisable to use freesurfer recons produced with 5.2. There was a bug in that version, which is why 5.3 was released shortly after 5.2: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes

Hope this helps, a.y

On Tue, 18 Mar 2014, McGinnity, Colm wrote:

Dear Anastasia,

Hello, many thanks for your quick reply, sorry for the delay.

I have switched to 3-column format and that does indeed get the process a little further, so many thanks for that. Unfortunately however I get this new error during the trac-all -bedp stage:

An exception has been thrown ERROR: Could not open image /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/data_slice_0000 Trace:read_volume4DROI.

I saw that similar errors had been identified in the past, but I wasn't really clear from the dialogue what the cause was or how to correct. Could you explain, please?

I have tried to run bedpostx directly as previously advised, it seems to be running at present. IF it is successful, can I just always do this instead and then continue with trac-all -path? Or do I need to use trac-all -bedp specifically?

Many thanks in advance, Best wishes, Colm.

Colm McGinnity King's College London

-----Original Message----- From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] Sent: 11 March 2014 00:39 To: McGinnity, Colm Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0

Hi Colm - Note that the information in the tutorial (particularly the part where gradient tables can be formatted in 3 rows or 3 columns) pertains to the latest tracula update: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

You're using an older version that only supports the 3-column format. I have no idea if this is what's causing the error without looking at your trac-all.log, but this would be a first guess.

a.y

On Mon, 10 Mar 2014, McGinnity, Colm wrote:

...

Dear Experts,   I am very new to TRACULA, I apologise for what is probably a silly question.   I’ve got the following error on running trac-all –prep (FreeSurfer 5.2.0):   awk: cmd. line:1: fatal: cannot open file `0' for reading (No such file or directory) mri_concat --i /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz --mean --o /home/k1193186/ FreeSurfer/TRACULA/ROLAND03A/dmri/lowb.nii.gz niiRead(): error opening file /home/k1193186/ FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz   Can anyone tell me what this means and how to fix this, please? I’m guessing I’ve set up my configuration wrong or have the files in the wrong place?   Many thanks! Best wishes, Colm. King's College London

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.

Hi Colm - The final version used is bvecs. The eddy current correction step registers each DWI to the first b=0 image, and the same transformation is applied to the corresponding gradient vector. This is a standard procedure when doing eddy current correction by registration.

Hope this helps, a.y

On Fri, 16 May 2014, McGinnity, Colm wrote:

Hi Anastasia,

Many thanks for your help. I did reply but don't see the email on the forum.

I have began using FreeSurfer 5.3.0 instead, thanks. However, I'm a bit confused - I've created a 3-column bvecs format file (I had been using for version 5.2.0).

After running several I've noticed the 'bvecs' file in the dmri folder is slightly different from the input file, whereas the 'bvecs.norot' file matches the input file extactly.

For example: File 2: 0.9200842 0.3251221 0.2185593 File 2: 0.919 0.3311 0.2141

Can you please clarify which is used, and if these differences can be ignored?

Thanks and best wishes, Colm.

-----Original Message----- From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] Sent: 11 March 2014 00:39 To: McGinnity, Colm Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0

Hi Colm - Note that the information in the tutorial (particularly the part where gradient tables can be formatted in 3 rows or 3 columns) pertains to the latest tracula update: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

You're using an older version that only supports the 3-column format. I have no idea if this is what's causing the error without looking at your trac-all.log, but this would be a first guess.

a.y

On Mon, 10 Mar 2014, McGinnity, Colm wrote:

...

Dear Experts,   I am very new to TRACULA, I apologise for what is probably a silly question.   I’ve got the following error on running trac-all –prep (FreeSurfer 5.2.0):   awk: cmd. line:1: fatal: cannot open file `0' for reading (No such file or directory) mri_concat --i /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz --mean --o /home/k1193186/ FreeSurfer/TRACULA/ROLAND03A/dmri/lowb.nii.gz niiRead(): error opening file /home/k1193186/ FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz   Can anyone tell me what this means and how to fix this, please? I’m guessing I’ve set up my configuration wrong or have the files in the wrong place?   Many thanks! Best wishes, Colm. King's College London

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.

btw, you are strongly encouraged NOT to use FS 5.2. For TRACULA it is probably fine, but we found some small but systematic problems with the anatomical analysis in 5.2 doug

On 05/16/2014 11:51 AM, McGinnity, Colm wrote:

Hi Anastasia,

Many thanks for your help. I did reply but don't see the email on the forum.

I have began using FreeSurfer 5.3.0 instead, thanks. However, I'm a bit confused - I've created a 3-column bvecs format file (I had been using for version 5.2.0).

After running several I've noticed the 'bvecs' file in the dmri folder is slightly different from the input file, whereas the 'bvecs.norot' file matches the input file extactly.

For example: File 2: 0.9200842 0.3251221 0.2185593 File 2: 0.919 0.3311 0.2141

Can you please clarify which is used, and if these differences can be ignored?

Thanks and best wishes, Colm.

-----Original Message----- From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] Sent: 11 March 2014 00:39 To: McGinnity, Colm Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0

Hi Colm - Note that the information in the tutorial (particularly the part where gradient tables can be formatted in 3 rows or 3 columns) pertains to the latest tracula update: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

You're using an older version that only supports the 3-column format. I have no idea if this is what's causing the error without looking at your trac-all.log, but this would be a first guess.

a.y

On Mon, 10 Mar 2014, McGinnity, Colm wrote:

...

Dear Experts,

I am very new to TRACULA, I apologise for what is probably a silly question.

I’ve got the following error on running trac-all –prep (FreeSurfer 5.2.0):

awk: cmd. line:1: fatal: cannot open file `0' for reading (No such file or directory) mri_concat --i /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz --mean --o /home/k1193186/ FreeSurfer/TRACULA/ROLAND03A/dmri/lowb.nii.gz niiRead(): error opening file /home/k1193186/ FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz

Can anyone tell me what this means and how to fix this, please? I’m guessing I’ve set up my configuration wrong or have the files in the wrong place?

Many thanks! Best wishes, Colm. King's College London

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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