Oh, right, I remember now (at least mostly). I fixed that for version 5.2. Maryam, it may be that the code is not actually using the persession data like it should. doug

On 01/22/2013 03:19 PM, raij@nmr.mgh.harvard.edu wrote:

Hi Doug,

There at least used to be a bug in the way perrun/persession was handled. We exchanged emails about that about a years ago (see especially Tapsya's emails). If I recall correctly we were never able to make this work without rigging the file extensions etc (FS-FAST always defaulted to one stream and/or one file extension regardless of which option was used). Not sure if this is still a problem, but could be related to Maryam's email.

Cheers,

Tommi

...

Hi Maryam, when you say that they are practically identical, I assume that there are at least some small differences indicating that something was different? And what are you comparing exactly? Eg, single subject or group? In principle, they should be pretty close to each other, it depends entirely on how much the subject moved between runs and how much smoothing you apply. If you have a well-behaved population, then there might not be much of a difference. If you reduce the smoothing to 0, then you might start to see more of an effect.

doug

On 01/22/2013 02:44 PM, Maryam Vaziri Pashkam wrote:

...

Hi Dough,

This might be a very basic question: I would like to compare the results of an analysis with the perrun and persession motion correction. Here is my analysis line:

*mkanalysis-sess *

*-analysis Cat_all_new -fsd bold -runlistfile runlist_all.txt *

*-native -mcextreg -stc siemens -fwhm 0 *

*-event-related -paradigm para_cat.par -nconditions 5 *

*-spmhrf 0 -TR 2 -refeventdur 4 -polyfit 2*

And here is what I have in my analysis info

analysis Cat_1 mcstem fmc fsd bold runlistfile run_1.txt TR 2 RegDOF 6 RawSpace volume native mask brain RawFWHM 0 RawSTC siemens UseB0DC 0 inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 nconditions 5 parname para_cat.par RefEventDur 3 timewindow 40.000000 prestim 0 TER 0.050000 spmhrf 0 stimulusdelay -1.00000000000000000000 Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 Condition 5 Condition05 nuisreg mcextreg 3

I preprocessed my data once using the perrun option and once using the persession option in two different directories and ran the analysis on both of those data sets. The problem is when the analysis finished the results where practically identical. I am not sure what is going on and can't figure out if the analysis in both cases is done based on the persession motion correction or they are both done based on the perrun motion correction and how I can get the analysis to run in two different ways. I am using freesurfer 5.1.

M

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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