Oh, ok. That's a known issue, it has to do with changes in the command line of the latest version of bedpostx. We've updated trac-all and it'll be working in our next release but for now you'll have to run bedpostx by itself and not through trac-all. Sorry for the inconvenience!

On Fri, 23 Mar 2012, Chris Watson wrote:

[freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/ dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz th1samples.nii.gz

Come to think of it, when I ran bedpostx, it only output "1 slice processed", but repeated 70 times, or however many slices there are. The data is from a Siemens 3T, by the way.

On 03/23/2012 01:16 PM, Anastasia Yendiki wrote:

...

What's in the diff_slices directory? That's a temporary directory that bedpostx creates and that gets deleted after the results get "merged". So my guess would be that bedpostx didn't finish processing.

On Fri, 23 Mar 2012, Chris Watson wrote:

...

Hello, I successfully ran trac-all -bedp, and when I run the next step I get the following error:

Loading BEDPOST parameter samples from /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX niiRead(): error opening file /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz

ERROR: Could not read /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz

Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux

trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012

Word too long.

Indeed, the "merged" file doesn't exist. I am running Freesurfer 5.1.0 and FSL 4.1.9. Here's what's in the dmri.bedpostX directory:

[freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ bvals bvecs commands.txt diff_slices logs monitor nodif_brain_mask.nii.gz xfms

---

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.

Yes.

On Fri, 23 Mar 2012, Chris Watson wrote:

Ok. Do I run it with the defaults? # fibers per voxel = 2 ARD weight = 1 burn-in period = 1000 # jumps = 1250 sample every = 25

On 03/23/2012 01:22 PM, Anastasia Yendiki wrote:

...

Oh, ok. That's a known issue, it has to do with changes in the command line of the latest version of bedpostx. We've updated trac-all and it'll be working in our next release but for now you'll have to run bedpostx by itself and not through trac-all. Sorry for the inconvenience!

On Fri, 23 Mar 2012, Chris Watson wrote:

...

[freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/ dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz th1samples.nii.gz

Come to think of it, when I ran bedpostx, it only output "1 slice processed", but repeated 70 times, or however many slices there are. The data is from a Siemens 3T, by the way.

On 03/23/2012 01:16 PM, Anastasia Yendiki wrote:

...

What's in the diff_slices directory? That's a temporary directory that bedpostx creates and that gets deleted after the results get "merged". So my guess would be that bedpostx didn't finish processing.

On Fri, 23 Mar 2012, Chris Watson wrote:

...

Hello, I successfully ran trac-all -bedp, and when I run the next

step I

...

get the following error:

...

Loading BEDPOST parameter samples from

/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX

...

niiRead(): error opening file

/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz

...

...

ERROR: Could not read

/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz

...

...

Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed

Mar 7

...

04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux

...

trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 Word too long.

---

...

...

Indeed, the "merged" file doesn't exist. I am running

Freesurfer 5.1.0

...

and FSL 4.1.9. Here's what's in the dmri.bedpostX directory:

...

[freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/

bvals bvecs commands.txt diff_slices logs monitor nodif_brain_mask.nii.gz xfms

...

---

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.

Hi Chris,

The diff_slices folder is still there, which means that bedpostX probably did not finish processing. That folder usually gets deleted after bedpostX processing completes. It's strange that you have merged_ph2samples.nii.gz and not merged_ph1samples.nii.gz.

Did you accidentally run bedpostX twice and exit out of it in the middle? It is quite possible that you'd already finished processing bedpostX(and all files were properly created) and started running it again, which would explain the diff_slices and the absence of merged_ph1samples (but not merged_ph2samples).

You could potentially back up your current bedpostx folder and re-run bedpostX to see if that solves your issue.

Could you also send the commandline you're using for bedpostX?

Thanks, Priti

Hi, I'm getting the same error as before; "merged_ph1samples.nii.gz" isn't getting created, I think. This is after I ran bedpostx on its own, per your instructions from this thread.

Here are the last few lines of output from trac-all -path: Loading BEDPOST parameter samples from /raid2/fmri8/control/H008B/dmri.bedpostX niiRead(): error opening file /raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read /raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz /parietal/freesurfer/current/bin/dmri_mergepaths --indir /raid2/fmri8/control/H008B/dpath --in --out /raid2/fmri8/control/H008B/dpath/merged_avg33_mni_bbr.mgz --ctab /parietal/freesurfer/current/FreeSurferColorLUT.txt --thresh .15 ERROR: must specify input volume(s)

This is what's in "dmri.bedpostX": bvals diff_slices logs mean_ph2samples.nii.gz merged_f2samples.nii.gz monitor bvecs dyads2_dispersion.nii.gz mean_dsamples.nii.gz mean_S0samples.nii.gz merged_ph2samples.nii.gz nodif_brain_mask.nii.gz commands.txt dyads2.nii.gz mean_f2samples.nii.gz mean_th2samples.nii.gz merged_th2samples.nii.gz xfms

Thanks, Chris

On 03/23/2012 01:25 PM, Anastasia Yendiki wrote:

...

Yes.

On Fri, 23 Mar 2012, Chris Watson wrote:

...

Ok. Do I run it with the defaults? # fibers per voxel = 2 ARD weight = 1 burn-in period = 1000 # jumps = 1250 sample every = 25

On 03/23/2012 01:22 PM, Anastasia Yendiki wrote:

...

Oh, ok. That's a known issue, it has to do with changes in the command line of the latest version of bedpostx. We've updated trac-all and it'll be working in our next release but for now you'll have to run bedpostx by itself and not through trac-all. Sorry for the inconvenience!

On Fri, 23 Mar 2012, Chris Watson wrote:

...

[freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/ dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz th1samples.nii.gz

Come to think of it, when I ran bedpostx, it only output "1 slice processed", but repeated 70 times, or however many slices there are. The data is from a Siemens 3T, by the way.

On 03/23/2012 01:16 PM, Anastasia Yendiki wrote:

...

What's in the diff_slices directory? That's a temporary directory that bedpostx creates and that gets deleted after the results get "merged". So my guess would be that bedpostx didn't finish processing.

On Fri, 23 Mar 2012, Chris Watson wrote:

> Hello, I successfully ran trac-all -bedp, and when I run the > next step I > get the following error: >> Loading BEDPOST parameter samples from /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX > niiRead(): error opening file > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >> ERROR: Could not read /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >> Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 > 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux >> trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012

>> Word too long.

>> Indeed, the "merged" file doesn't exist. I am running Freesurfer 5.1.0 > and FSL 4.1.9. > Here's what's in the dmri.bedpostX directory: >> [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ > bvals bvecs commands.txt diff_slices logs monitor > nodif_brain_mask.nii.gz xfms >> _______________________________________________ > 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

So I'm assuming that you don't have any issues merged_ph* files anymore?

As far as the error below is concerned, this is typically the last step in trac-paths, where it should merge all the 18 tracts to create a 4D tract volume for visualization. The input for this should be all the 18 posterior distribution volumes. From what I see below, it does not look like the tract reconstruction finished for any of the tracts (which is why --in is empty). If you send us the trac-all.log, I can take a look. Also do you see any tract volumes under dpath/ ?

Hope that helps, Priti

Yes, I figured out that I had previously run "trac-all -bedp" and it created "data_slice_0002". I deleted this directory, and bedpostx finished, but now I get this error from "trac-all-path": Segmentation fault (core dumped) /parietal/freesurfer/current/bin/dmri_mergepaths --indir /raid2/fmri8/control/H008B/dpath --in --out /raid2/fmri8/control/H008B/dpath/merged_avg33_mni_bbr.mgz --ctab /parietal/freesurfer/current/FreeSurferColorLUT.txt --thresh .15 ERROR: must specify input volume(s)

What should be specified here?

Thanks, Chris

PS When running bedpostx I was simply using the defaults, so "bedpostx H008B/dmri.bedpostX" was the command line.

On 05/07/2012 02:28 PM, Priti Srinivasan wrote:

...

Hi Chris,

The diff_slices folder is still there, which means that bedpostX probably did not finish processing. That folder usually gets deleted after bedpostX processing completes. It's strange that you have merged_ph2samples.nii.gz and not merged_ph1samples.nii.gz.

Did you accidentally run bedpostX twice and exit out of it in the middle? It is quite possible that you'd already finished processing bedpostX(and all files were properly created) and started running it again, which would explain the diff_slices and the absence of merged_ph1samples (but not merged_ph2samples).

You could potentially back up your current bedpostx folder and re-run bedpostX to see if that solves your issue.

Could you also send the commandline you're using for bedpostX?

Thanks, Priti

...

Hi, I'm getting the same error as before; "merged_ph1samples.nii.gz" isn't getting created, I think. This is after I ran bedpostx on its own, per your instructions from this thread.

Here are the last few lines of output from trac-all -path: Loading BEDPOST parameter samples from /raid2/fmri8/control/H008B/dmri.bedpostX niiRead(): error opening file /raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read /raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz /parietal/freesurfer/current/bin/dmri_mergepaths --indir /raid2/fmri8/control/H008B/dpath --in --out /raid2/fmri8/control/H008B/dpath/merged_avg33_mni_bbr.mgz --ctab /parietal/freesurfer/current/FreeSurferColorLUT.txt --thresh .15 ERROR: must specify input volume(s)

This is what's in "dmri.bedpostX": bvals diff_slices logs mean_ph2samples.nii.gz merged_f2samples.nii.gz monitor bvecs dyads2_dispersion.nii.gz mean_dsamples.nii.gz mean_S0samples.nii.gz merged_ph2samples.nii.gz nodif_brain_mask.nii.gz commands.txt dyads2.nii.gz mean_f2samples.nii.gz mean_th2samples.nii.gz merged_th2samples.nii.gz xfms

Thanks, Chris

On 03/23/2012 01:25 PM, Anastasia Yendiki wrote:

...

Yes.

On Fri, 23 Mar 2012, Chris Watson wrote:

...

Ok. Do I run it with the defaults? # fibers per voxel = 2 ARD weight = 1 burn-in period = 1000 # jumps = 1250 sample every = 25

On 03/23/2012 01:22 PM, Anastasia Yendiki wrote:

...

Oh, ok. That's a known issue, it has to do with changes in the command line of the latest version of bedpostx. We've updated trac-all and it'll be working in our next release but for now you'll have to run bedpostx by itself and not through trac-all. Sorry for the inconvenience!

On Fri, 23 Mar 2012, Chris Watson wrote:

> [freesurfer@occipital dmri.bedpostX]$ ls > diff_slices/data_slice_0002/ > dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz > mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz > th1samples.nii.gz > > > Come to think of it, when I ran bedpostx, it only output "1 > slice > processed", but repeated 70 times, or however many slices there > are. The > data is from a Siemens 3T, by the way. > > On 03/23/2012 01:16 PM, Anastasia Yendiki wrote: >> What's in the diff_slices directory? That's a temporary >> directory >> that >> bedpostx creates and that gets deleted after the results get >> "merged". So >> my guess would be that bedpostx didn't finish processing. >> >> On Fri, 23 Mar 2012, Chris Watson wrote: >> >>> Hello, I successfully ran trac-all -bedp, and when I run the >>> next >> step I >>> get the following error: >>>> Loading BEDPOST parameter samples from >> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX >>> niiRead(): error opening file >>> >> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >>>> ERROR: Could not read >> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >>>> Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP >>>> Wed >> Mar 7 >>> 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux >>>> trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT >>>> 2012 >>>> Word too long. >> ------------------------------------------------------------------------ >> >>>> Indeed, the "merged" file doesn't exist. I am running >> Freesurfer 5.1.0 >>> and FSL 4.1.9. >>> Here's what's in the dmri.bedpostX directory: >>>> [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ >>> bvals bvecs commands.txt diff_slices logs monitor >>> nodif_brain_mask.nii.gz xfms >>>> _______________________________________________ >>> 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