Hi,

I have scans from a Philips scanner I want to process with FreeSurfer. Previously, the scans have been downloaded in the Philips PAR/REC format and converted into niftis, and those niftis have been used as the raw inputs in other imaging pipelines.

Instead of dredging up the original dicoms and unpacking from scratch (I’ve been trying to but I’m running into a variety of problems), will the whole FreeSurfer pipeline work if I simply take the niftis I already have, manually create dirs specifying the FreeSurfer hierarchy of session/fsd/run, and stick the nifti inside the run dir? (I’ve already tried this and I’m running into problems during preprocessing, and I’m not sure if it’s because I need to unpack from scratch with dcmunpack, or if I have bugs in preprocessing.)

Thanks, Stephanie

Right, I can run recon-all for the structural run. But what about for a functional run where all I have is one nifti per subject? I meant for preprocessing etc. the functional things, if I manually create the hierarchy, is that one raw .nii per subject enough info to carry out the rest of the pipeline? Or do I need to find a way to dcmunpack the functional run, or something else?

Thanks, Steph

On Jun 2, 2018, at 8:04 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Stephanie

you shouldn't have to create the directory structure or anything. If you have nifti files you can give those to recon-all as input in the same way you would dicom (with -i <nifti volume file) and it will create the directories and do it's thing

cheers Bruce On Sat, 2 Jun 2018, DeCross, Stephanie N. wrote:

...

Hi,

I have scans from a Philips scanner I want to process with FreeSurfer. Previously, the scans have been downloaded in the Philips PAR/REC format and converted into niftis, and those niftis have been used as the raw inputs in other imaging pipelines.

Instead of dredging up the original dicoms and unpacking from scratch (I’ve been trying to but I’m running into a variety of problems), will the whole FreeSurfer pipeline work if I simply take the niftis I already have, manually create dirs specifying the FreeSurfer hierarchy of session/fsd/run, and stick the nifti inside the run dir? (I’ve already tried this and I’m running into problems during preprocessing, and I’m not sure if it’s because I need to unpack from scratch with dcmunpack, or if I have bugs in preprocessing.)

Thanks, Stephanie

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OK, I realized that I was running under Freesurfer 5.3 and not 6.0. Once I was running under the correct version, things were running as intended.

I was told that in fs-fast, motion correction (mc) has to go before slice timing correction (stc). For my data, I need to run stc before mc. So I found this work around method: What I did was to run slice timing correction by running stc-sess on the .nii files, rename these stc corrected files back to its original name (and thus pretended they were the original files), and then run preproc-sess without stc. Everything seemed to run through so far to the GLM stage. Does this work around sound OK? Would it cause any problem in the analysis down the line?

Thanks a lot, - Yaoda

On Jun 1, 2018, at 6:43 PM, Xu, Yaoda <yaodaxu@wjh.harvard.edumailto:yaodaxu@wjh.harvard.edu> wrote:

I tried to use preprocess-sess with -sdf, here is the error message:

ERROR: Flag -sdf unrecognized.

I attach here the slice timing. I saved it in a .txt file and tried “-sdf slicetimingfile” but got the above error message.

Instead of using preproc-sess directly, I tried to use stc-sess to correct for timing and then planned to rename the file to the appropriate name to use preproc-sess. But stc-sess would not take -sdf either. In theory, these steps should allow me to do STC first and then MC in fs-fast, right?

Here is the slice timing: slice time no. (ms)

1 0.0 2 772.5 3 65.0 4 837.5 5 127.5 6 900.0 7 192.5 8 965.0 9 257.5 10 1030.0 11 322.5 12 1092.5 13 385.0 14 1157.5 15 450.0 16 1222.5 17 515.0 18 1287.5 19 580.0 20 1350.0 21 642.5 22 1415.0 23 707.5 24 0.0 25 772.5 26 65.0 27 837.5 28 127.5 29 900.0 30 192.5 31 965.0 32 257.5 33 1030.0 34 322.5 35 1092.5 36 385.0 37 1157.5 38 450.0 39 1222.5 40 515.0 41 1287.5 42 580.0 43 1350.0 44 642.5 45 1415.0 46 707.5 47 0.0 48 772.5 49 65.0 50 837.5 51 127.5 52 900.0 53 192.5 54 965.0 55 257.5 56 1030.0 57 322.5 58 1092.5 59 385.0 60 1157.5 61 450.0 62 1222.5 63 515.0 64 1287.5 65 580.0 66 1350.0 67 642.5 68 1415.0 69 707.5

Thanks, - Yaoda

On Jun 1, 2018, at 5:21 PM, Douglas Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> wrote:

You will need to know how many slice groups were used in the acquisition, fsfast will not know that. preproc-sess should accept a slice-timing with with -sdf (though this is not listed in the help). What is the error that you are getting? There is no way to do STC before MC in fsfast. When you have interleaved slices, there are arguments for each order (when the slices are acquired continguously, then MC should always go first).

On 5/31/18 11:42 PM, Xu, Yaoda wrote: Dear all,

I am trying to do slicing timing correcting with Siemens’s 3T Prisma data at acceleration 3. I am told that I can use “-ngroups” when running "preproc-sess”. How do I use the “-ngroups” flag? Should I do “-ngroups 3”? Would fs-fast automatically compute the slice timing file and apply it accordingly? I have the actual slice timing file. I tried to use "-sdf slicedelayfile”, but it does not seem to be a recognized flag.

It appears that fs-fast does slice timing correction after motion correction. If the volume is going to be resliced after motion correction, thus each slice will no longer have its original timing, shouldn’t slice timing correction be done before motion correction? Is there a way in fs-fast to run slice timing correction before motion correction? I guess instead of running “preproc-sess”, I could first run “sts-sess” and then “mc-sess”?

Any suggestions would be greatly appreciated. Thank you!

- Yaoda Xu

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Great to know that this would not cause any problems. After I did stc first and named the file with the stc stem, I tried to use -mcin, -mcout, -smin, and -smout to specific the input and output file stems for motion correction and spatial smoothing in preproc-sess. I received error messages about some files not being there, etc. So I just renamed the stc files back to f.nii.gz files and then ran preproc-sess. Everything seemed to work. So I think renaming seems to work the best if one does not want to disturb things too much.

On Jun 6, 2018, at 12:46 AM, Douglas Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> wrote:

That sounds ok, I don't think it will cause problems. You can also do whatever preprocessing you want and then specify the input data with the -funcstem option to mkanalysis-sess

On 6/5/18 8:16 PM, Xu, Yaoda wrote: OK, I realized that I was running under Freesurfer 5.3 and not 6.0. Once I was running under the correct version, things were running as intended.

I was told that in fs-fast, motion correction (mc) has to go before slice timing correction (stc). For my data, I need to run stc before mc. So I found this work around method: What I did was to run slice timing correction by running stc-sess on the .nii files, rename these stc corrected files back to its original name (and thus pretended they were the original files), and then run preproc-sess without stc. Everything seemed to run through so far to the GLM stage. Does this work around sound OK? Would it cause any problem in the analysis down the line?

Thanks a lot, - Yaoda

On Jun 1, 2018, at 6:43 PM, Xu, Yaoda <yaodaxu@wjh.harvard.edumailto:yaodaxu@wjh.harvard.edu> wrote:

I tried to use preprocess-sess with -sdf, here is the error message:

ERROR: Flag -sdf unrecognized.

I attach here the slice timing. I saved it in a .txt file and tried “-sdf slicetimingfile” but got the above error message.

Instead of using preproc-sess directly, I tried to use stc-sess to correct for timing and then planned to rename the file to the appropriate name to use preproc-sess. But stc-sess would not take -sdf either. In theory, these steps should allow me to do STC first and then MC in fs-fast, right?

Here is the slice timing: slice time no. (ms)

1 0.0 2 772.5 3 65.0 4 837.5 5 127.5 6 900.0 7 192.5 8 965.0 9 257.5 10 1030.0 11 322.5 12 1092.5 13 385.0 14 1157.5 15 450.0 16 1222.5 17 515.0 18 1287.5 19 580.0 20 1350.0 21 642.5 22 1415.0 23 707.5 24 0.0 25 772.5 26 65.0 27 837.5 28 127.5 29 900.0 30 192.5 31 965.0 32 257.5 33 1030.0 34 322.5 35 1092.5 36 385.0 37 1157.5 38 450.0 39 1222.5 40 515.0 41 1287.5 42 580.0 43 1350.0 44 642.5 45 1415.0 46 707.5 47 0.0 48 772.5 49 65.0 50 837.5 51 127.5 52 900.0 53 192.5 54 965.0 55 257.5 56 1030.0 57 322.5 58 1092.5 59 385.0 60 1157.5 61 450.0 62 1222.5 63 515.0 64 1287.5 65 580.0 66 1350.0 67 642.5 68 1415.0 69 707.5

Thanks, - Yaoda

On Jun 1, 2018, at 5:21 PM, Douglas Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> wrote:

You will need to know how many slice groups were used in the acquisition, fsfast will not know that. preproc-sess should accept a slice-timing with with -sdf (though this is not listed in the help). What is the error that you are getting? There is no way to do STC before MC in fsfast. When you have interleaved slices, there are arguments for each order (when the slices are acquired continguously, then MC should always go first).

On 5/31/18 11:42 PM, Xu, Yaoda wrote: Dear all,

I am trying to do slicing timing correcting with Siemens’s 3T Prisma data at acceleration 3. I am told that I can use “-ngroups” when running "preproc-sess”. How do I use the “-ngroups” flag? Should I do “-ngroups 3”? Would fs-fast automatically compute the slice timing file and apply it accordingly? I have the actual slice timing file. I tried to use "-sdf slicedelayfile”, but it does not seem to be a recognized flag.

It appears that fs-fast does slice timing correction after motion correction. If the volume is going to be resliced after motion correction, thus each slice will no longer have its original timing, shouldn’t slice timing correction be done before motion correction? Is there a way in fs-fast to run slice timing correction before motion correction? I guess instead of running “preproc-sess”, I could first run “sts-sess” and then “mc-sess”?

Any suggestions would be greatly appreciated. Thank you!

- Yaoda Xu

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